Analysis of the Broad’s Avana CRISPR (Broad Institute Cancer Dependency Map 2018, Meyers et al. 2017) and the Broad and Dana-Farber Cancer Institite’s Achilles shRNA (MacFarland et al. 2018, Data Science 2018).
The Avana screen produced results using CERES (Meyers et al. 2017) (GitHub), which generates gene dependency scores from sgRNA depletion scores from gene essentiality screens and eliminates bias arising from the effect of copy number variation on Cas9 DNA cleavage. The lower the CERES score, the higher the likelihood that the gene is essential in the associated cell line. Scores are scaled per cell line such that a score of 0 is the median effect of nonessential genes and -1 is the median effect of common core essential genes.
All annotation files (copy number, mutation status, and gene expression) (Consortium and Consortium 2015, Barretina et al. 2012) were downloaded from the DepMap Data Portal.
library(bsselectR)
library(data.table)
library(ggpubr)
library(ggsignif)
library(kableExtra)
library(tidyverse)
adj_signif <- function(df) {
# Takes df from compare_means and creates a signif code column for adjusted p-vals
df$p.signif <- ifelse(df$p.signif == "ns", NA, df$p.signif)
df$p.signif.adj <- ifelse(df$p.adj <= 0.0001, "****",
ifelse(df$p.adj <= 0.001, "***",
ifelse(df$p.adj <= 0.01, "**",
ifelse(df$p.adj <= 0.05, "*", NA))))
df$p.short <- formatC(df$p, format = "g", digits = 2)
df$p.adj.short <- formatC(df$p.adj, format = "g", digits = 2)
return(df)
}
WilcoxonByDrug <- function(drug, dataset, data_name) {
use_data <- filter(dataset, Drug == drug)
sig <- compare_means(AUC ~ Mutation_Status_Nonsilent, group.by = "Hugo_Symbol", data = use_data, method = "wilcox.test", p.adjust.method = "BH")
sig <- adj_signif(sig)
sig <- sig[order(sig$p),]
sig$Drug <- drug
sig$Dataset <- data_name
return(sig)
}
makeDrugBoxplots <- function(drug, dataset) {
if(dataset == "CCLE" | dataset == "ccle") {
use_data <- filter(ccle_data_g2p_genesfilt, Drug == drug)
use_color <- as.character(use_data$Color_Nonsilent)
names(use_color) <- use_data$Mutation_Status_Nonsilent
sig <- ccle_signif_g2p_ByDrug[[drug]]
label_text <- data.frame(p.signif = sig$p.signif, p.signif.adj = sig$p.signif.adj, Hugo_Symbol = sig$Hugo_Symbol)
label_text$Hugo_Symbol <- factor(label_text$Hugo_Symbol, levels = g2p_genes)
}
else if(dataset == "CTRP" | dataset == "ctrp") {
use_data <- filter(ctrp_data_g2p_genesfilt, Drug == drug)
use_color <- as.character(use_data$Color_Nonsilent)
names(use_color) <- use_data$Mutation_Status_Nonsilent
sig <- ctrp_signif_g2p_ByDrug[[drug]]
label_text <- data.frame(p.signif = sig$p.signif, p.signif.adj = sig$p.signif.adj, Hugo_Symbol = sig$Hugo_Symbol)
label_text$Hugo_Symbol <- factor(label_text$Hugo_Symbol, levels = g2p_genes)
}
else if(dataset == "GDSC" | dataset == "gdsc") {
use_data <- filter(gdsc_data_g2p_genesfilt, Drug == drug)
use_color <- as.character(use_data$Color_Nonsilent)
names(use_color) <- use_data$Mutation_Status_Nonsilent
sig <- gdsc_signif_g2p_ByDrug[[drug]]
label_text <- data.frame(p.signif = sig$p.signif, p.signif.adj = sig$p.signif.adj, Hugo_Symbol = sig$Hugo_Symbol)
label_text$Hugo_Symbol <- factor(label_text$Hugo_Symbol, levels = g2p_genes)
}
else { return("Error: Invalid dataset.") }
plot <- ggplot(data = use_data, aes(x = Mutation_Status_Nonsilent, y = AUC)) +
facet_wrap(~ Hugo_Symbol, drop = FALSE, nrow = 1) +
geom_boxplot(mapping = aes(fill = Mutation_Status_Nonsilent), position = position_dodge(0.85), outlier.shape = 3, outlier.size = 0.5) +
scale_fill_manual(values = use_color) +
guides(color = FALSE) +
geom_text(data = label_text, mapping = aes(x = 1.5, y = max(use_data$AUC), label = p.signif), nudge_y = 0.2) +
theme(legend.position = "top", axis.ticks.x = element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank()) +
labs(fill = "Mutation Status", y = "AUC", x = "Mutation Status", title = paste0(toupper(dataset), ": ", drug))
return(plot)
}
This comprehensive cancer cell line information curated by Daniel Charytonowicz.
ccl_converter <- read.delim("./data_munging/cell_line_database_v1_20180911.tsv", row.names = 1, sep = "\t", header = TRUE)
ccl_info <- read.delim("./data_munging/DepMap-2018q3-celllines.csv", sep = ",", header = TRUE, na.strings = c("", NA))
ccl_info$Primary.Disease <- gsub("\\\\", "", ccl_info$Primary.Disease)
ccl_info$Primary.Disease <- gsub("Ewings", "Ewing's", ccl_info$Primary.Disease)
# From figshare
crispr_meta <- read.delim("./data_munging/sample_info_18Q3_crispr.csv", sep = ",", header = TRUE, na.strings = c("", NA))
colnames(crispr_meta)[7] <- "CCLE_Name"
For mutation calling, get paired gene name and cell line fields in a data frame. For this analysis, we don’t care about how many mutations there are per gene or what type of mutations there are, so I didn’t save more information. I took unique gene-cell line combinations since we only cared about mutation presence/absence. Add a Mutation_Status column denoting all entries in MAF files as mutations present in the associated cell lines.
maf_raw <- read.delim("./data_munging/CCLE_DepMap_18q3_maf_20180718.txt.gz", header = TRUE, sep = "\t")
# Filter for cell lines in CRISPR screen
maf_raw <- filter(maf_raw, Broad_ID %in% unique(crispr_meta$Broad_ID))
colnames(maf_raw)[colnames(maf_raw) == "Tumor_Sample_Barcode"] <- "CCLE_Name"
# Select columns
maf_df <- subset(maf_raw, select = c("Hugo_Symbol", "CCLE_Name", "Broad_ID", "Variant_Classification", "Reference_Allele", "Tumor_Seq_Allele1"))
maf_df$Reference_Allele_Length <- ifelse(maf_df$Reference_Allele == "-", 0, nchar(as.character(maf_df$Reference_Allele)))
maf_df$Tumor_Seq_Allele1_Length <- nchar(as.character(maf_df$Tumor_Seq_Allele1))
# Add Mutation_Status column
maf_df$Mutation_Status_Nonsilent <- ifelse(maf_df$Variant_Classification == "Silent", "Other", "Mutant")
maf_df <- unique(subset(maf_df, select = c("Hugo_Symbol", "CCLE_Name", "Broad_ID", "Mutation_Status_Nonsilent", "Reference_Allele_Length", "Tumor_Seq_Allele1_Length")))
cn <- read.delim("./data_munging/public_18Q3_gene_cn_v2.csv.gz", sep = ",", check.names = FALSE, header = TRUE)
# Convert log2 ratios (log2(CN/2)) to CN
cn[2:ncol(cn)] <- lapply(cn[2:ncol(cn)], function(x) 2 * (2 ^ x))
# Remove Entrez gene IDs from colnames
colnames(cn) <- gsub(" .*", "", colnames(cn))
colnames(cn)[1] <- "Broad_ID"
# Melt
cn_melt <- melt(data = cn, id.vars = "Broad_ID", measure.vars = colnames(cn[2:ncol(cn)]), variable.name = "Hugo_Symbol", value.name = "Copy_Number")
saveRDS(cn_melt, "./data_munging/rds/cn_melt_18Q3.rds", compress = "xz")
cn_melt <- readRDS("./data_munging/rds/cn_melt_18Q3.rds")
Gene expression data (Reads Per Kilobase of transcript, per Million mapped reads, RPKM).
ge <- read.delim("./../crispr_lineages_giant_files/CCLE_DepMap_18q3_RNAseq_RPKM_20180718.gct.gz", skip = 2, header = TRUE, sep = "\t", check.names = FALSE)
# Edit columns
ge$Name <- NULL
colnames(ge)[1] <- "Hugo_Symbol"
# Melt
ge_melt <- melt(data = ge, id.vars = "Hugo_Symbol", measure.vars = colnames(ge[2:ncol(ge)]), value.name = "RPKM")
## Split variable column
ge_melt <- with(ge_melt, cbind(Hugo_Symbol, colsplit(variable, pattern = " ", names = c("CCLE_Name", "Broad_ID")), RPKM))
## Remove parentheses around Broad IDs
ge_melt$Broad_ID <- gsub("\\(|\\)", "", ge_melt$Broad_ID)
saveRDS(ge_melt, "./../crispr_lineages_giant_files/ge_melt_18Q3.rds", compress = "xz")
ge_melt <- readRDS("./../crispr_lineages_giant_files/ge_melt_18Q3.rds")
g2p <- read.delim("./data_munging/g2p_full_level_A_dataset_v2_10_10_2018.tsv", sep = "\t", header = TRUE)
g2p$Drug <- tolower(g2p$Drug)
g2p$Drug_Gene <- ifelse(is.na(g2p$Drug) | is.na(g2p$Gene), NA, paste0(g2p$Drug, "_", g2p$Gene))
g2p <- subset(g2p, grepl("^CID", g2p$DrugID))
g2p_drug_genes <- as.character(unique(g2p$Drug_Gene[!is.na(g2p$Drug_Gene)]))
g2p_genes <- unique(sapply(strsplit(g2p_drug_genes, "_", fixed = TRUE), function(x) x[2]))
g2p_drugs <- unique(sapply(strsplit(g2p_drug_genes, "_", fixed = TRUE), function(x) x[1]))
g2p_genes
## [1] "ALK" "EGFR" "PDGFRA" "JAK2" "KIT" "ABL1" "BRAF"
## [8] "BRCA1" "DPYD" "G6PD" "TSC2" "UGT1A1" "IDH2" "PDGFRB"
## [15] "MET" "ERBB3" "KRAS" "RET" "ROS1" "ESR1" "ERBB2"
## [22] "BRCA2" "PML" "TPMT" "TSC1" "MGMT" "PDGFB" "AKT1"
## [29] "MYD88" "PTCH1" "DNMT3A" "CYP19A1" "FLT3" "NPM1"
g2p_drugs
## [1] "ceritinib" "crizotinib"
## [3] "gefitinib" "afatinib"
## [5] "imatinib" "ruxolitinib"
## [7] "sunitinib" "regorafenib"
## [9] "dasatinib" "ponatinib"
## [11] "brigatinib" "vemurafenib"
## [13] "trametinib" "cobimetinib"
## [15] "olaparib" "2-fluoropyrimidine"
## [17] "erlotinib" "osimertinib"
## [19] "dabrafenib" "everolimus"
## [21] "nilotinib" "capecitabine"
## [23] "enasidenib" "icotinib"
## [25] "cabozantinib" "fluorouracil"
## [27] "fulvestrant" "lapatinib"
## [29] "azd" "alectinib"
## [31] "rucaparib" "niraparib"
## [33] "docetaxel" "tretinoin"
## [35] "purine" "guanine"
## [37] "temozolomide" "pralidoxime mesylate"
## [39] "nafomine malate" "neratinib"
## [41] "ap26113" "bosutinib monohydrate"
## [43] "tegafur" "arsenic"
## [45] "irinotecan" "vandetanib"
## [47] "letrozole" "ibrutinib"
## [49] "vismodegib" "daunorubicin"
## [51] "pazopanib" "belinostat"
## [53] "anastrozole" "midostaurin"
## [55] "cyclophosphamide" "selumetinib"
## [57] "palbociclib"
# Order and genes taken from pink heatmapo from Daniel's analyses
g2p_genes <- c("KRAS", "EGFR", "MET", "ALK", "BRAF", "ERBB2", "ABL1", "ROS1", "KIT", "DPYD", "PDGFRA", "RET", "BRCA1", "UGT1A1", "IDH2", "ESR1", "TPMT", "BRCA2", "PDGFRB", "G6PD", "PML", "TSC1", "FLT3", "ERBB3", "CYP19A1", "AKT1", "PTCH1", "MGMT", "DNMT3A", "MYD88", "PDGFB", "TSC2", "NPM1", "JAK2")
dep <- read.delim("./data_munging/gene_dependency_18Q3.csv.gz", sep = ",", header = TRUE, check.names = FALSE)
# Remove Entrez gene IDs from colnames
colnames(dep) <- gsub(" .*", "", colnames(dep))
The latest CRISPR CERES score data (18Q3, August 2018) was pulled from the DepMap Data Portal (Broad Institute Cancer Dependency Map 2018, Meyers et al. 2017).
crispr <- read.delim("./data_munging/gene_effect_18Q3.csv.gz", sep = ",", header = TRUE, check.names = FALSE)
# Remove Entrez gene IDs from colnames
colnames(crispr) <- gsub(" .*", "", colnames(crispr))
Merge annotation data:
# Melt CRISPR dataset for merging
crispr_melt <- melt(crispr, id.vars = "Broad_ID", measure.vars = colnames(crispr)[2:ncol(crispr)], variable.name = "Hugo_Symbol", value.name = "Score")
# Melt dependency probabilities dataset for merging
dep_melt <- melt(dep, id.vars = "Broad_ID", measure.vars = colnames(dep)[2:ncol(dep)], variable.name = "Hugo_Symbol", value.name = "Dep_Prob")
# Merge dependency probabilities
crispr_melt <- merge(crispr_melt, dep_melt, by = c("Broad_ID", "Hugo_Symbol"), all.x = TRUE)
# Merge cell line metadata
crispr_melt <- merge(crispr_melt, ccl_info, by = "Broad_ID", all.x = TRUE)
crispr_melt <- merge(crispr_melt, crispr_meta, by = c("CCLE_Name", "Broad_ID"), all.x = TRUE)
# Merge mutation annotations
crispr_muts <- merge(crispr_melt, maf_df, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
crispr_muts$Hugo_Symbol <- factor(crispr_muts$Hugo_Symbol)
crispr_muts <- crispr_muts %>% mutate(Mutation_Status_Nonsilent = if_else(is.na(Mutation_Status_Nonsilent), "Other", Mutation_Status_Nonsilent))
# Summarize number of mutant and Other cell lines
crispr_muts_summ <- crispr_muts %>% group_by(Hugo_Symbol) %>%
summarize(N_Nonsilent_Other = sum(Mutation_Status_Nonsilent == "Other"),
N_Nonsilent_Mutant = sum(Mutation_Status_Nonsilent == "Mutant"))
# Merge test results back into full dataset, which restores information lost in the summarization
crispr_data <- merge(crispr_muts_summ, crispr_muts, by = "Hugo_Symbol")
# Add Color columns
crispr_data$Color_Nonsilent <- ifelse(crispr_data$Mutation_Status_Nonsilent == "Other", "thistle", "darkorchid")
crispr_data$Color_Nonsilent <- factor(crispr_data$Color_Nonsilent)
# Cell line lineages
crispr_data <- merge(crispr_data, ccl_converter, by = c("CCLE_Name", "Broad_ID"), all.x = TRUE)
levels(crispr_data$lineage_name) <- sort(levels(crispr_data$lineage_name), decreasing = TRUE)
# Copy number
crispr_data <- merge(crispr_data, cn_melt, by = c("Hugo_Symbol", "Broad_ID"), all.x = TRUE)
# Gene expression (RPKM)
ge_filt <- filter(ge_melt, Hugo_Symbol %in% unique(crispr_data$Hugo_Symbol) & Broad_ID %in% unique(crispr_data$Broad_ID))
crispr_data <- merge(crispr_data, ge_filt, by = c("Hugo_Symbol", "Broad_ID", "CCLE_Name"), all.x = TRUE)
crispr_data$RPKM_log2 <- log2(crispr_data$RPKM + 0.0001)
saveRDS(crispr_data, "./../crispr_lineages_giant_files/crispr_data_18Q3.rds", compress = "xz")
crispr_data <- readRDS("./../crispr_lineages_giant_files/crispr_data_18Q3.rds")
crispr_data_ptmuts <- filter(crispr_data, Reference_Allele_Length == 1 | Reference_Allele_Length == 0 | is.na(Reference_Allele_Length))
crispr_data_ptmuts$Keep_PtMut_Tests <- ifelse(crispr_data_ptmuts$Reference_Allele_Length == 1 | is.na(crispr_data_ptmuts$Reference_Allele_Length), TRUE, ifelse(crispr_data_ptmuts$Tumor_Seq_Allele1_Length == 1, TRUE, FALSE))
crispr_data_ptmuts <- filter(crispr_data_ptmuts, Keep_PtMut_Tests == TRUE)
# Filter CRISPR for G2P genes in G2P
crispr_data_g2p <- filter(crispr_data_ptmuts, Hugo_Symbol %in% g2p_genes)
crispr_data_g2p$Hugo_Symbol <- factor(crispr_data_g2p$Hugo_Symbol, levels = g2p_genes)
# Drug metadata
drug_meta <- read.delim("./data_munging/drug_id_drug_name_table_10_12_2018.tsv", sep = "\t", header = FALSE)
colnames(drug_meta) <- c("CID", "Drug")
drug_meta$Drug <- tolower(drug_meta$Drug)
maf_df_g2p <- filter(maf_df, Hugo_Symbol %in% g2p_genes)
# CCLE
ccle <- read.delim("./data_munging/data_drug_auc_ccle_10_12_2018.csv", sep = "\t", header = TRUE, row.names = 1, check.names = FALSE)
ccle <- merge(drug_meta, ccle, by = "CID")
ccle_melt <- melt(ccle, id.vars = c("CID", "Drug"), measure.vars = colnames(ccle)[3:ncol(ccle)], variable.name = "accession_id", value.name = "AUC")
ccle_grid <- expand.grid("accession_id" = unique(ccle_melt$accession_id), "Hugo_Symbol" = g2p_genes)
ccle_data <- merge(ccle_grid, ccle_melt, by = "accession_id", all.x = TRUE)
ccle_data <- merge(ccle_data, ccl_converter, by = "accession_id", all.x = TRUE)
ccle_data <- merge(ccle_data, maf_df_g2p, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
ccle_data$Mutation_Status_Nonsilent <- ifelse(is.na(ccle_data$Mutation_Status_Nonsilent), "Other", ccle_data$Mutation_Status_Nonsilent)
ccle_data$Hugo_Symbol <- factor(ccle_data$Hugo_Symbol)
ccle_data$AUC <- as.numeric(ccle_data$AUC)
ccle_data$Color_Nonsilent <- ifelse(ccle_data$Mutation_Status_Nonsilent == "Other", "palegreen3", "springgreen4")
ccle_data$Color_Nonsilent <- factor(ccle_data$Color_Nonsilent)
ccle_data <- filter(ccle_data, !is.na(ccle_data$AUC))
ccle_data$Drug_Gene <- paste0(ccle_data$Drug, "_", ccle_data$Hugo_Symbol)
saveRDS(ccle_data, "./data_munging/rds/ccle_data_18Q3.rds", compress = "xz")
# CTRP
ctrp <- read.delim("./data_munging/data_drug_auc_ctrp_10_12_2018.csv", sep = "\t", header = TRUE, row.names = 1, check.names = FALSE)
ctrp <- merge(drug_meta, ctrp, by = "CID")
ctrp_melt <- melt(ctrp, id.vars = c("CID", "Drug"), measure.vars = colnames(ctrp)[3:ncol(ctrp)], variable.name = "accession_id", value.name = "AUC")
ctrp_grid <- expand.grid("accession_id" = unique(ctrp_melt$accession_id), "Hugo_Symbol" = g2p_genes)
ctrp_data <- merge(ctrp_grid, ctrp_melt, by = "accession_id", all.x = TRUE)
ctrp_data <- merge(ctrp_data, ccl_converter, by = "accession_id", all.x = TRUE)
ctrp_data <- merge(ctrp_data, maf_df_g2p, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
ctrp_data$Mutation_Status_Nonsilent <- ifelse(is.na(ctrp_data$Mutation_Status_Nonsilent), "Other", ctrp_data$Mutation_Status_Nonsilent)
ctrp_data$Hugo_Symbol <- factor(ctrp_data$Hugo_Symbol)
ctrp_data$AUC <- as.numeric(ctrp_data$AUC)
ctrp_data$Color_Nonsilent <- ifelse(ctrp_data$Mutation_Status_Nonsilent == "Other", "slategray3", "steelblue4")
ctrp_data$Color_Nonsilent <- factor(ctrp_data$Color_Nonsilent)
ctrp_data <- filter(ctrp_data, !is.na(ctrp_data$AUC))
ctrp_data$Drug_Gene <- paste0(ctrp_data$Drug, "_", ctrp_data$Hugo_Symbol)
saveRDS(ctrp_data, "./data_munging/rds/ctrp_data_18Q3.rds", compress = "xz")
# GDSC
gdsc <- read.delim("./data_munging/data_drug_auc_gdsc_10_12_2018.csv", sep = "\t", header = TRUE, row.names = 1, check.names = FALSE)
gdsc <- merge(drug_meta, gdsc, by = "CID")
gdsc_melt <- melt(gdsc, id.vars = c("CID", "Drug"), measure.vars = colnames(gdsc)[3:ncol(gdsc)], variable.name = "accession_id", value.name = "AUC")
gdsc_grid <- expand.grid("accession_id" = unique(gdsc_melt$accession_id), "Hugo_Symbol" = g2p_genes)
gdsc_data <- merge(gdsc_grid, gdsc_melt, by = "accession_id", all.x = TRUE)
gdsc_data <- merge(gdsc_data, ccl_converter, by = "accession_id", all.x = TRUE)
gdsc_data <- merge(gdsc_data, maf_df_g2p, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
gdsc_data$Mutation_Status_Nonsilent <- ifelse(is.na(gdsc_data$Mutation_Status_Nonsilent), "Other", gdsc_data$Mutation_Status_Nonsilent)
gdsc_data$Hugo_Symbol <- factor(gdsc_data$Hugo_Symbol)
gdsc_data$AUC <- as.numeric(gdsc_data$AUC)
gdsc_data$Color_Nonsilent <- ifelse(gdsc_data$Mutation_Status_Nonsilent == "Other", "paleturquoise3", "turquoise4")
gdsc_data$Color_Nonsilent <- factor(gdsc_data$Color_Nonsilent)
gdsc_data <- filter(gdsc_data, !is.na(gdsc_data$AUC))
gdsc_data$Drug_Gene <- paste0(gdsc_data$Drug, "_", gdsc_data$Hugo_Symbol)
saveRDS(gdsc_data, "./data_munging/rds/gdsc_data_18Q3.rds", compress = "xz")
ccle_data <- readRDS("./data_munging/rds/ccle_data_18Q3.rds")
ccle_data_ptmuts <- filter(ccle_data, Reference_Allele_Length == 1 | Reference_Allele_Length == 0 | is.na(Reference_Allele_Length))
ccle_data_ptmuts$Keep_PtMut_Tests <- ifelse(ccle_data_ptmuts$Reference_Allele_Length == 1 | is.na(ccle_data_ptmuts$Reference_Allele_Length), TRUE, ifelse(ccle_data_ptmuts$Tumor_Seq_Allele1_Length == 1, TRUE, FALSE))
ccle_data_ptmuts <- filter(ccle_data_ptmuts, Keep_PtMut_Tests == TRUE)
ctrp_data <- readRDS("./data_munging/rds/ctrp_data_18Q3.rds")
ctrp_data_ptmuts <- filter(ctrp_data, Reference_Allele_Length == 1 | Reference_Allele_Length == 0 | is.na(Reference_Allele_Length))
ctrp_data_ptmuts$Keep_PtMut_Tests <- ifelse(ctrp_data_ptmuts$Reference_Allele_Length == 1 | is.na(ctrp_data_ptmuts$Reference_Allele_Length), TRUE, ifelse(ctrp_data_ptmuts$Tumor_Seq_Allele1_Length == 1, TRUE, FALSE))
ctrp_data_ptmuts <- filter(ctrp_data_ptmuts, Keep_PtMut_Tests == TRUE)
gdsc_data <- readRDS("./data_munging/rds/gdsc_data_18Q3.rds")
gdsc_data_ptmuts <- filter(gdsc_data, Reference_Allele_Length == 1 | Reference_Allele_Length == 0 | is.na(Reference_Allele_Length))
gdsc_data_ptmuts$Keep_PtMut_Tests <- ifelse(gdsc_data_ptmuts$Reference_Allele_Length == 1 | is.na(gdsc_data_ptmuts$Reference_Allele_Length), TRUE, ifelse(gdsc_data_ptmuts$Tumor_Seq_Allele1_Length == 1, TRUE, FALSE))
gdsc_data_ptmuts <- filter(gdsc_data_ptmuts, Keep_PtMut_Tests == TRUE)
# Filter drug screen datasets for G2P drug-gene associations
ccle_data_g2p <- filter(ccle_data_ptmuts, Drug_Gene %in% g2p_drug_genes)
ctrp_data_g2p <- filter(ctrp_data_ptmuts, Drug_Gene %in% g2p_drug_genes)
gdsc_data_g2p <- filter(gdsc_data_ptmuts, Drug_Gene %in% g2p_drug_genes)
# Filter drug screen datasets for G2P genes in drug-gene associations
ccle_data_g2p_genesfilt <- filter(ccle_data_ptmuts, Hugo_Symbol %in% g2p_genes)
ccle_data_g2p_genesfilt$Hugo_Symbol <- ordered(ccle_data_g2p_genesfilt$Hugo_Symbol, levels = g2p_genes)
ctrp_data_g2p_genesfilt <- filter(ctrp_data_ptmuts, Hugo_Symbol %in% g2p_genes)
ctrp_data_g2p_genesfilt$Hugo_Symbol <- ordered(ctrp_data_g2p_genesfilt$Hugo_Symbol, levels = g2p_genes)
gdsc_data_g2p_genesfilt <- filter(gdsc_data_ptmuts, Hugo_Symbol %in% g2p_genes)
gdsc_data_g2p_genesfilt$Hugo_Symbol <- ordered(gdsc_data_g2p_genesfilt$Hugo_Symbol, levels = g2p_genes)
crispr_data_g2p_summ <- unique(crispr_data_g2p[, c("Hugo_Symbol", "N_Nonsilent_Mutant", "N_Nonsilent_Other")])
crispr_data_g2p_summ$Fraction_Mutant <- crispr_data_g2p_summ$N_Nonsilent_Mutant / (crispr_data_g2p_summ$N_Nonsilent_Mutant + crispr_data_g2p_summ$N_Nonsilent_Other)
crispr_data_g2p_summ$Percent_Mutant <- crispr_data_g2p_summ$Fraction_Mutant * 100
# write.table(crispr_data_g2p_summ, file = "~/Desktop/crispr_data_g2p_summ_20181003.tsv", quote = FALSE, sep = "\t")
crispr_signif_g2p_gene <- compare_means(Score ~ Mutation_Status_Nonsilent, group.by = c("Hugo_Symbol"), data = crispr_data_g2p, method = "wilcox.test", p.adjust.method = "BH")
crispr_signif_g2p_gene <- adj_signif(crispr_signif_g2p_gene)
crispr_signif_g2p_gene <- crispr_signif_g2p_gene[order(crispr_signif_g2p_gene$p),]
saveRDS(crispr_signif_g2p_gene, "./data_munging/rds/crispr_signif_g2p_gene.rds")
crispr_signif_g2p_gene <- readRDS("./data_munging/rds/crispr_signif_g2p_gene.rds")
crispr_signif_g2p_20gene <- as.character(crispr_signif_g2p_gene$Hugo_Symbol[0:20])
knitr::kable(filter(crispr_signif_g2p_gene, p < 0.1)[, c("Hugo_Symbol", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "Wilcoxon test results for Level A point mutations, p < 0.01 (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|
| KRAS | 0.0000000 | 0.0000000 | <2e-16 | **** | **** |
| NRAS | 0.0000000 | 0.0000000 | <2e-16 | **** | **** |
| BRAF | 0.0000000 | 0.0000000 | <2e-16 | **** | **** |
| TSC2 | 0.0123492 | 0.1099118 | 0.012 |
|
NA |
| JAK2 | 0.0164691 | 0.1099118 | 0.016 |
|
NA |
| UGT1A1 | 0.0173545 | 0.1099118 | 0.017 |
|
NA |
| CYP19A1 | 0.0266336 | 0.1445822 | 0.027 |
|
NA |
| DPYD | 0.0395906 | 0.1880553 | 0.040 |
|
NA |
crispr_data_signif_g2p_gene_filt <- filter(crispr_data_ptmuts, Hugo_Symbol %in% crispr_signif_g2p_20gene)
crispr_data_signif_g2p_gene <- merge(crispr_data_signif_g2p_gene_filt, crispr_signif_g2p_gene, by = "Hugo_Symbol")
crispr_data_signif_g2p_gene$Hugo_Symbol <- ordered(crispr_data_signif_g2p_gene$Hugo_Symbol, levels = crispr_signif_g2p_20gene)
crispr_data_signif_g2p_gene_color <- as.character(crispr_data_signif_g2p_gene$Color_Nonsilent)
names(crispr_data_signif_g2p_gene_color) <- crispr_data_signif_g2p_gene$Mutation_Status_Nonsilent
crispr_data_signif_g2p_gene <- merge(crispr_data_signif_g2p_gene, crispr_data_signif_g2p_gene %>% group_by(Hugo_Symbol) %>% summarize(Text_y = max(Score)), by = "Hugo_Symbol")
crispr_data_signif_g2p_gene_text <- unique(data.frame(p.signif = crispr_data_signif_g2p_gene$p.signif, p.signif.adj = crispr_data_signif_g2p_gene$p.signif.adj, Hugo_Symbol = crispr_data_signif_g2p_gene$Hugo_Symbol, Text_y = crispr_data_signif_g2p_gene$Text_y))
crispr_data_signif_g2p_gene_plot <- ggplot(data = crispr_data_signif_g2p_gene, aes(x = Mutation_Status_Nonsilent, y = Score)) +
facet_wrap(~ Hugo_Symbol, nrow = 2, scales = "free_y") +
geom_jitter(aes(color = Mutation_Status_Nonsilent), alpha = 0.5, width = 0.3) +
geom_boxplot(color = "black", fill = NA, outlier.shape = NA) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
scale_color_manual(values = crispr_data_signif_g2p_gene_color) +
geom_text(data = crispr_data_signif_g2p_gene_text, mapping = aes(x = 1.5, y = Text_y, label = p.signif), nudge_y = 0.2) +
theme(legend.position = "top") +
labs(y = "CERES Score",
x = "Lineage",
color = "Mutation Status",
title = "CERES scores for select Level A G2P genes",
subtitle = "Genes are sorted by increasing p-value.")
crispr_data_signif_g2p_gene_plot
# Genes with adjusted p-values < 0.3 are shown.\nBH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001\n
# ggsave("./plots_18Q3/manuscript/crispr_data_signif_g2p_gene_plot.png", crispr_data_signif_g2p_gene_plot, width = 12, height = 7, units = "in")
crispr_signif_g2p_lineage <- compare_means(Score ~ Mutation_Status_Nonsilent, group.by = c("Hugo_Symbol", "group_general_lineage_name"), data = crispr_data_g2p, method = "wilcox.test", p.adjust.method = "BH")
crispr_signif_g2p_lineage <- adj_signif(crispr_signif_g2p_lineage)
crispr_signif_g2p_lineage <- crispr_signif_g2p_lineage[order(crispr_signif_g2p_lineage$p),]
saveRDS(crispr_signif_g2p_lineage, "./data_munging/rds/crispr_signif_g2p_lineage.rds")
# write.table(crispr_signif_g2p_lineage, file = "~/Desktop/crispr_signif_g2p_lineage.csv", quote = FALSE, sep = ",", row.names = FALSE)
crispr_signif_g2p_lineage <- readRDS("./data_munging/rds/crispr_signif_g2p_lineage.rds")
knitr::kable(filter(crispr_signif_g2p_lineage, p < 0.01)[, c("Hugo_Symbol", "group_general_lineage_name", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "Wilcoxon test results comparing non-silent mutant vs other cell lines by lineage, p < 0.01 (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | group_general_lineage_name | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|---|
| KRAS | lung cancer | 0.0000000 | 0.0000030 | 2.5e-09 | **** | **** |
| TP53 | lung cancer | 0.0000086 | 0.0049934 | 8.6e-06 | **** | ** |
| TP53 | central nervous system cancer | 0.0000504 | 0.0195615 | 5.0e-05 | **** |
|
| KRAS | ovarian cancer | 0.0001488 | 0.0433268 | 0.00015 | *** |
|
| TP53 | ovarian cancer | 0.0002837 | 0.0661128 | 0.00028 | *** | NA |
| NRAS | leukemia | 0.0005316 | 0.1032138 | 0.00053 | *** | NA |
| PIK3CA | ovarian cancer | 0.0008371 | 0.1365241 | 0.00084 | *** | NA |
| PIK3CA | breast cancer | 0.0009842 | 0.1365241 | 0.00098 | *** | NA |
| KRAS | colorectal cancer | 0.0010547 | 0.1365241 | 0.00105 | ** | NA |
| NRAS | multiple myeloma | 0.0013756 | 0.1602564 | 0.00138 | ** | NA |
| NRAS | skin cancer | 0.0016637 | 0.1762022 | 0.00166 | ** | NA |
| TP53 | leukemia | 0.0023741 | 0.2304810 | 0.00237 | ** | NA |
| PTEN | ovarian cancer | 0.0032141 | 0.2733311 | 0.00321 | ** | NA |
| TP53 | colorectal cancer | 0.0036603 | 0.2733311 | 0.00366 | ** | NA |
| TP53 | skin cancer | 0.0037227 | 0.2733311 | 0.00372 | ** | NA |
| VHL | kidney cancer | 0.0037539 | 0.2733311 | 0.00375 | ** | NA |
| KRAS | stomach cancer | 0.0040001 | 0.2741275 | 0.00400 | ** | NA |
| BRAF | skin cancer | 0.0054870 | 0.3419998 | 0.00549 | ** | NA |
| SETD2 | kidney cancer | 0.0056647 | 0.3419998 | 0.00566 | ** | NA |
| PTEN | central nervous system cancer | 0.0059869 | 0.3419998 | 0.00599 | ** | NA |
| ASXL1 | colorectal cancer | 0.0061648 | 0.3419998 | 0.00616 | ** | NA |
| PIK3CA | colorectal cancer | 0.0070506 | 0.3733617 | 0.00705 | ** | NA |
| PTEN | uterine cancer | 0.0080389 | 0.4071865 | 0.00804 | ** | NA |
crispr_data_signif_g2p_lineage <- merge(crispr_data_signif_g2p_gene_filt, crispr_signif_g2p_lineage, by = c("Hugo_Symbol", "group_general_lineage_name"))
crispr_data_signif_g2p_lineage$Hugo_Symbol <- ordered(crispr_data_signif_g2p_lineage$Hugo_Symbol, levels = crispr_signif_g2p_20gene)
crispr_data_signif_g2p_lineage_color <- as.character(crispr_data_signif_g2p_lineage$Color_Nonsilent)
names(crispr_data_signif_g2p_lineage_color) <- crispr_data_signif_g2p_lineage$Mutation_Status_Nonsilent
crispr_data_signif_g2p_lineage <- merge(crispr_data_signif_g2p_lineage, crispr_data_signif_g2p_lineage %>% group_by(Hugo_Symbol) %>% summarize(Text_y = max(Score)), by = "Hugo_Symbol")
crispr_data_signif_g2p_lineage_text <- unique(data.frame(p.signif = crispr_data_signif_g2p_lineage$p.signif, p.signif.adj = crispr_data_signif_g2p_lineage$p.signif.adj, group_general_lineage_name = crispr_data_signif_g2p_lineage$group_general_lineage_name, Hugo_Symbol = crispr_data_signif_g2p_lineage$Hugo_Symbol, Text_y = crispr_data_signif_g2p_lineage$Text_y))
crispr_data_signif_g2p_lineage_plot <- ggplot(data = crispr_data_signif_g2p_lineage, aes(x = group_general_lineage_name, y = Score)) +
facet_wrap(~ Hugo_Symbol, nrow = 4, scales = "free_y") +
geom_point(aes(color = Mutation_Status_Nonsilent), alpha = 0.5) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
scale_color_manual(values = crispr_data_signif_g2p_lineage_color) +
geom_text(data = crispr_data_signif_g2p_lineage_text, mapping = aes(x = group_general_lineage_name, y = Text_y, label = p.signif), angle = 90, nudge_y = 0.1) +
theme(legend.position = "top", axis.text.x = element_text(angle = 90, hjust = 1, vjust = 1, size = 10)) +
labs(y = "CERES Score",
x = "Lineage",
color = "Mutation Status",
title = "CERES score by cell line lineage for significant Level A G2P genes",
subtitle = "Genes with adjusted p-values < 0.3 are shown.\nBH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001\nGenes are sorted by increasing lineage-agnostic p-value.")
crispr_data_signif_g2p_lineage_plot
# ggsave("./plots_18Q3/manuscript/crispr_crispr_data_signif_g2p_lineage_plot.png", crispr_data_signif_g2p_lineage_plot, width = 12, height = 15, units = "in")
crispr_data_signif_g2p_lineage_summ <- crispr_data_signif_g2p_lineage %>% group_by(Hugo_Symbol, group_general_lineage_name, Mutation_Status_Nonsilent) %>% tally()
# write.table(crispr_data_signif_g2p_lineage_summ, file = "~/Desktop/crispr_data_signif_g2p_lineage_summ_20181005.tsv", quote = FALSE, sep = "\t")
knitr::kable(crispr_data_signif_g2p_lineage_summ, caption = "Mutant/Other counts for gene-lineage combinations") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | group_general_lineage_name | Mutation_Status_Nonsilent | n |
|---|---|---|---|
| KRAS | bone cancer | Mutant | 1 |
| KRAS | bone cancer | Other | 15 |
| KRAS | breast cancer | Mutant | 2 |
| KRAS | breast cancer | Other | 24 |
| KRAS | colorectal cancer | Mutant | 14 |
| KRAS | colorectal cancer | Other | 13 |
| KRAS | esophageal cancer | Mutant | 1 |
| KRAS | esophageal cancer | Other | 13 |
| KRAS | leukemia | Mutant | 2 |
| KRAS | leukemia | Other | 19 |
| KRAS | lung cancer | Mutant | 22 |
| KRAS | lung cancer | Other | 48 |
| KRAS | multiple myeloma | Mutant | 4 |
| KRAS | multiple myeloma | Other | 12 |
| KRAS | ovarian cancer | Mutant | 9 |
| KRAS | ovarian cancer | Other | 26 |
| KRAS | pancreatic cancer | Mutant | 23 |
| KRAS | pancreatic cancer | Other | 1 |
| KRAS | stomach cancer | Mutant | 5 |
| KRAS | stomach cancer | Other | 10 |
| KRAS | urinary bladder cancer | Mutant | 2 |
| KRAS | urinary bladder cancer | Other | 19 |
| KRAS | uterine cancer | Mutant | 7 |
| KRAS | uterine cancer | Other | 11 |
| NRAS | bone cancer | Mutant | 1 |
| NRAS | bone cancer | Other | 15 |
| NRAS | cancer | Mutant | 2 |
| NRAS | cancer | Other | 16 |
| NRAS | central nervous system cancer | Mutant | 2 |
| NRAS | central nervous system cancer | Other | 43 |
| NRAS | head and neck cancer | Mutant | 1 |
| NRAS | head and neck cancer | Other | 14 |
| NRAS | leukemia | Mutant | 6 |
| NRAS | leukemia | Other | 15 |
| NRAS | lung cancer | Mutant | 5 |
| NRAS | lung cancer | Other | 65 |
| NRAS | lymphoma | Mutant | 2 |
| NRAS | lymphoma | Other | 9 |
| NRAS | multiple myeloma | Mutant | 6 |
| NRAS | multiple myeloma | Other | 10 |
| NRAS | peripheral nervous system neoplasm | Mutant | 2 |
| NRAS | peripheral nervous system neoplasm | Other | 11 |
| NRAS | rhabdomyosarcoma | Mutant | 1 |
| NRAS | rhabdomyosarcoma | Other | 6 |
| NRAS | skin cancer | Mutant | 5 |
| NRAS | skin cancer | Other | 25 |
| NRAS | urinary bladder cancer | Mutant | 4 |
| NRAS | urinary bladder cancer | Other | 17 |
| NRAS | uterine cancer | Mutant | 3 |
| NRAS | uterine cancer | Other | 15 |
| BRAF | bone cancer | Mutant | 1 |
| BRAF | bone cancer | Other | 14 |
| BRAF | breast cancer | Mutant | 3 |
| BRAF | breast cancer | Other | 22 |
| BRAF | cancer | Mutant | 2 |
| BRAF | cancer | Other | 16 |
| BRAF | central nervous system cancer | Mutant | 2 |
| BRAF | central nervous system cancer | Other | 43 |
| BRAF | colorectal cancer | Mutant | 13 |
| BRAF | colorectal cancer | Other | 15 |
| BRAF | esophageal cancer | Mutant | 2 |
| BRAF | esophageal cancer | Other | 12 |
| BRAF | liver cancer | Mutant | 1 |
| BRAF | liver cancer | Other | 15 |
| BRAF | lung cancer | Mutant | 3 |
| BRAF | lung cancer | Other | 66 |
| BRAF | multiple myeloma | Mutant | 2 |
| BRAF | multiple myeloma | Other | 14 |
| BRAF | ovarian cancer | Mutant | 3 |
| BRAF | ovarian cancer | Other | 31 |
| BRAF | pancreatic cancer | Mutant | 2 |
| BRAF | pancreatic cancer | Other | 21 |
| BRAF | peripheral nervous system neoplasm | Mutant | 1 |
| BRAF | peripheral nervous system neoplasm | Other | 12 |
| BRAF | skin cancer | Mutant | 23 |
| BRAF | skin cancer | Other | 8 |
| BRAF | stomach cancer | Mutant | 1 |
| BRAF | stomach cancer | Other | 14 |
| BRAF | thyroid cancer | Mutant | 1 |
| BRAF | thyroid cancer | Other | 2 |
| BRAF | urinary bladder cancer | Mutant | 1 |
| BRAF | urinary bladder cancer | Other | 20 |
| BRAF | uterine cancer | Mutant | 5 |
| BRAF | uterine cancer | Other | 14 |
| TSC2 | breast cancer | Mutant | 1 |
| TSC2 | breast cancer | Other | 25 |
| TSC2 | cancer | Mutant | 1 |
| TSC2 | cancer | Other | 17 |
| TSC2 | central nervous system cancer | Mutant | 1 |
| TSC2 | central nervous system cancer | Other | 43 |
| TSC2 | colorectal cancer | Mutant | 5 |
| TSC2 | colorectal cancer | Other | 22 |
| TSC2 | esophageal cancer | Mutant | 1 |
| TSC2 | esophageal cancer | Other | 13 |
| TSC2 | kidney cancer | Mutant | 1 |
| TSC2 | kidney cancer | Other | 21 |
| TSC2 | leukemia | Mutant | 2 |
| TSC2 | leukemia | Other | 19 |
| TSC2 | liver cancer | Mutant | 2 |
| TSC2 | liver cancer | Other | 14 |
| TSC2 | lymphoma | Mutant | 2 |
| TSC2 | lymphoma | Other | 9 |
| TSC2 | multiple myeloma | Mutant | 2 |
| TSC2 | multiple myeloma | Other | 14 |
| TSC2 | pancreatic cancer | Mutant | 2 |
| TSC2 | pancreatic cancer | Other | 21 |
| TSC2 | peripheral nervous system neoplasm | Mutant | 1 |
| TSC2 | peripheral nervous system neoplasm | Other | 12 |
| TSC2 | rhabdomyosarcoma | Mutant | 1 |
| TSC2 | rhabdomyosarcoma | Other | 6 |
| TSC2 | stomach cancer | Mutant | 2 |
| TSC2 | stomach cancer | Other | 13 |
| TSC2 | uterine cancer | Mutant | 9 |
| TSC2 | uterine cancer | Other | 10 |
| JAK2 | colorectal cancer | Mutant | 1 |
| JAK2 | colorectal cancer | Other | 27 |
| JAK2 | esophageal cancer | Mutant | 1 |
| JAK2 | esophageal cancer | Other | 13 |
| JAK2 | leukemia | Mutant | 1 |
| JAK2 | leukemia | Other | 20 |
| JAK2 | lung cancer | Mutant | 2 |
| JAK2 | lung cancer | Other | 67 |
| JAK2 | lymphoma | Mutant | 1 |
| JAK2 | lymphoma | Other | 10 |
| JAK2 | ovarian cancer | Mutant | 1 |
| JAK2 | ovarian cancer | Other | 34 |
| JAK2 | urinary bladder cancer | Mutant | 2 |
| JAK2 | urinary bladder cancer | Other | 19 |
| JAK2 | uterine cancer | Mutant | 5 |
| JAK2 | uterine cancer | Other | 13 |
| UGT1A1 | bone cancer | Mutant | 2 |
| UGT1A1 | bone cancer | Other | 14 |
| UGT1A1 | colorectal cancer | Mutant | 1 |
| UGT1A1 | colorectal cancer | Other | 25 |
| UGT1A1 | esophageal cancer | Mutant | 1 |
| UGT1A1 | esophageal cancer | Other | 13 |
| UGT1A1 | kidney cancer | Mutant | 1 |
| UGT1A1 | kidney cancer | Other | 21 |
| UGT1A1 | lung cancer | Mutant | 2 |
| UGT1A1 | lung cancer | Other | 67 |
| UGT1A1 | skin cancer | Mutant | 2 |
| UGT1A1 | skin cancer | Other | 28 |
| UGT1A1 | stomach cancer | Mutant | 1 |
| UGT1A1 | stomach cancer | Other | 14 |
| UGT1A1 | uterine cancer | Mutant | 3 |
| UGT1A1 | uterine cancer | Other | 16 |
| CYP19A1 | breast cancer | Mutant | 1 |
| CYP19A1 | breast cancer | Other | 25 |
| CYP19A1 | esophageal cancer | Mutant | 1 |
| CYP19A1 | esophageal cancer | Other | 13 |
| CYP19A1 | lymphoma | Mutant | 1 |
| CYP19A1 | lymphoma | Other | 10 |
| CYP19A1 | peripheral nervous system neoplasm | Mutant | 1 |
| CYP19A1 | peripheral nervous system neoplasm | Other | 12 |
| CYP19A1 | stomach cancer | Mutant | 1 |
| CYP19A1 | stomach cancer | Other | 14 |
| CYP19A1 | urinary bladder cancer | Mutant | 1 |
| CYP19A1 | urinary bladder cancer | Other | 20 |
| CYP19A1 | uterine cancer | Mutant | 2 |
| CYP19A1 | uterine cancer | Other | 16 |
| DPYD | bone cancer | Mutant | 1 |
| DPYD | bone cancer | Other | 15 |
| DPYD | breast cancer | Mutant | 2 |
| DPYD | breast cancer | Other | 24 |
| DPYD | central nervous system cancer | Mutant | 1 |
| DPYD | central nervous system cancer | Other | 44 |
| DPYD | colorectal cancer | Mutant | 4 |
| DPYD | colorectal cancer | Other | 24 |
| DPYD | head and neck cancer | Mutant | 1 |
| DPYD | head and neck cancer | Other | 14 |
| DPYD | kidney cancer | Mutant | 2 |
| DPYD | kidney cancer | Other | 20 |
| DPYD | leukemia | Mutant | 1 |
| DPYD | leukemia | Other | 21 |
| DPYD | liver cancer | Mutant | 1 |
| DPYD | liver cancer | Other | 15 |
| DPYD | lung cancer | Mutant | 4 |
| DPYD | lung cancer | Other | 65 |
| DPYD | lymphoma | Mutant | 1 |
| DPYD | lymphoma | Other | 10 |
| DPYD | multiple myeloma | Mutant | 1 |
| DPYD | multiple myeloma | Other | 15 |
| DPYD | ovarian cancer | Mutant | 2 |
| DPYD | ovarian cancer | Other | 33 |
| DPYD | rhabdomyosarcoma | Mutant | 1 |
| DPYD | rhabdomyosarcoma | Other | 6 |
| DPYD | skin cancer | Mutant | 4 |
| DPYD | skin cancer | Other | 25 |
| DPYD | urinary bladder cancer | Mutant | 1 |
| DPYD | urinary bladder cancer | Other | 20 |
| DPYD | uterine cancer | Mutant | 2 |
| DPYD | uterine cancer | Other | 16 |
| CD274 | esophageal cancer | Mutant | 1 |
| CD274 | esophageal cancer | Other | 13 |
| CD274 | liver cancer | Mutant | 1 |
| CD274 | liver cancer | Other | 15 |
| CD274 | ovarian cancer | Mutant | 1 |
| CD274 | ovarian cancer | Other | 34 |
| CD274 | urinary bladder cancer | Mutant | 1 |
| CD274 | urinary bladder cancer | Other | 20 |
| CD274 | uterine cancer | Mutant | 1 |
| CD274 | uterine cancer | Other | 17 |
| ERBB2 | breast cancer | Mutant | 1 |
| ERBB2 | breast cancer | Other | 25 |
| ERBB2 | colorectal cancer | Mutant | 3 |
| ERBB2 | colorectal cancer | Other | 25 |
| ERBB2 | head and neck cancer | Mutant | 1 |
| ERBB2 | head and neck cancer | Other | 14 |
| ERBB2 | kidney cancer | Mutant | 1 |
| ERBB2 | kidney cancer | Other | 21 |
| ERBB2 | leukemia | Mutant | 1 |
| ERBB2 | leukemia | Other | 20 |
| ERBB2 | lung cancer | Mutant | 3 |
| ERBB2 | lung cancer | Other | 66 |
| ERBB2 | ovarian cancer | Mutant | 2 |
| ERBB2 | ovarian cancer | Other | 33 |
| ERBB2 | stomach cancer | Mutant | 2 |
| ERBB2 | stomach cancer | Other | 13 |
| ERBB2 | urinary bladder cancer | Mutant | 2 |
| ERBB2 | urinary bladder cancer | Other | 20 |
| ERBB2 | uterine cancer | Mutant | 5 |
| ERBB2 | uterine cancer | Other | 14 |
| BRCA2 | bone cancer | Mutant | 1 |
| BRCA2 | bone cancer | Other | 15 |
| BRCA2 | breast cancer | Mutant | 5 |
| BRCA2 | breast cancer | Other | 21 |
| BRCA2 | cancer | Mutant | 3 |
| BRCA2 | cancer | Other | 15 |
| BRCA2 | central nervous system cancer | Mutant | 2 |
| BRCA2 | central nervous system cancer | Other | 43 |
| BRCA2 | colorectal cancer | Mutant | 7 |
| BRCA2 | colorectal cancer | Other | 22 |
| BRCA2 | esophageal cancer | Mutant | 2 |
| BRCA2 | esophageal cancer | Other | 12 |
| BRCA2 | kidney cancer | Mutant | 2 |
| BRCA2 | kidney cancer | Other | 20 |
| BRCA2 | leukemia | Mutant | 3 |
| BRCA2 | leukemia | Other | 18 |
| BRCA2 | liver cancer | Mutant | 1 |
| BRCA2 | liver cancer | Other | 15 |
| BRCA2 | lung cancer | Mutant | 6 |
| BRCA2 | lung cancer | Other | 63 |
| BRCA2 | multiple myeloma | Mutant | 1 |
| BRCA2 | multiple myeloma | Other | 15 |
| BRCA2 | ovarian cancer | Mutant | 2 |
| BRCA2 | ovarian cancer | Other | 33 |
| BRCA2 | pancreatic cancer | Mutant | 1 |
| BRCA2 | pancreatic cancer | Other | 22 |
| BRCA2 | skin cancer | Mutant | 6 |
| BRCA2 | skin cancer | Other | 23 |
| BRCA2 | stomach cancer | Mutant | 2 |
| BRCA2 | stomach cancer | Other | 13 |
| BRCA2 | uterine cancer | Mutant | 7 |
| BRCA2 | uterine cancer | Other | 15 |
| RET | bone cancer | Mutant | 1 |
| RET | bone cancer | Other | 15 |
| RET | cancer | Mutant | 2 |
| RET | cancer | Other | 16 |
| RET | central nervous system cancer | Mutant | 1 |
| RET | central nervous system cancer | Other | 44 |
| RET | colorectal cancer | Mutant | 2 |
| RET | colorectal cancer | Other | 25 |
| RET | esophageal cancer | Mutant | 1 |
| RET | esophageal cancer | Other | 13 |
| RET | kidney cancer | Mutant | 1 |
| RET | kidney cancer | Other | 21 |
| RET | leukemia | Mutant | 1 |
| RET | leukemia | Other | 20 |
| RET | lung cancer | Mutant | 5 |
| RET | lung cancer | Other | 64 |
| RET | ovarian cancer | Mutant | 2 |
| RET | ovarian cancer | Other | 33 |
| RET | skin cancer | Mutant | 2 |
| RET | skin cancer | Other | 27 |
| RET | uterine cancer | Mutant | 2 |
| RET | uterine cancer | Other | 16 |
| ALK | breast cancer | Mutant | 2 |
| ALK | breast cancer | Other | 24 |
| ALK | cancer | Mutant | 2 |
| ALK | cancer | Other | 16 |
| ALK | colorectal cancer | Mutant | 8 |
| ALK | colorectal cancer | Other | 20 |
| ALK | esophageal cancer | Mutant | 2 |
| ALK | esophageal cancer | Other | 12 |
| ALK | leukemia | Mutant | 3 |
| ALK | leukemia | Other | 18 |
| ALK | liver cancer | Mutant | 1 |
| ALK | liver cancer | Other | 15 |
| ALK | lung cancer | Mutant | 7 |
| ALK | lung cancer | Other | 63 |
| ALK | lymphoma | Mutant | 1 |
| ALK | lymphoma | Other | 10 |
| ALK | ovarian cancer | Mutant | 2 |
| ALK | ovarian cancer | Other | 33 |
| ALK | pancreatic cancer | Mutant | 1 |
| ALK | pancreatic cancer | Other | 22 |
| ALK | peripheral nervous system neoplasm | Mutant | 2 |
| ALK | peripheral nervous system neoplasm | Other | 11 |
| ALK | skin cancer | Mutant | 3 |
| ALK | skin cancer | Other | 26 |
| ALK | uterine cancer | Mutant | 3 |
| ALK | uterine cancer | Other | 16 |
| PDGFRA | breast cancer | Mutant | 1 |
| PDGFRA | breast cancer | Other | 25 |
| PDGFRA | cancer | Mutant | 1 |
| PDGFRA | cancer | Other | 17 |
| PDGFRA | central nervous system cancer | Mutant | 1 |
| PDGFRA | central nervous system cancer | Other | 44 |
| PDGFRA | colorectal cancer | Mutant | 3 |
| PDGFRA | colorectal cancer | Other | 24 |
| PDGFRA | esophageal cancer | Mutant | 1 |
| PDGFRA | esophageal cancer | Other | 13 |
| PDGFRA | kidney cancer | Mutant | 1 |
| PDGFRA | kidney cancer | Other | 21 |
| PDGFRA | leukemia | Mutant | 3 |
| PDGFRA | leukemia | Other | 18 |
| PDGFRA | lung cancer | Mutant | 8 |
| PDGFRA | lung cancer | Other | 63 |
| PDGFRA | ovarian cancer | Mutant | 1 |
| PDGFRA | ovarian cancer | Other | 34 |
| PDGFRA | pancreatic cancer | Mutant | 1 |
| PDGFRA | pancreatic cancer | Other | 22 |
| PDGFRA | skin cancer | Mutant | 3 |
| PDGFRA | skin cancer | Other | 26 |
| PDGFRA | urinary bladder cancer | Mutant | 2 |
| PDGFRA | urinary bladder cancer | Other | 19 |
| PDGFRA | uterine cancer | Mutant | 4 |
| PDGFRA | uterine cancer | Other | 14 |
| BRCA1 | breast cancer | Mutant | 2 |
| BRCA1 | breast cancer | Other | 23 |
| BRCA1 | colorectal cancer | Mutant | 5 |
| BRCA1 | colorectal cancer | Other | 23 |
| BRCA1 | head and neck cancer | Mutant | 1 |
| BRCA1 | head and neck cancer | Other | 14 |
| BRCA1 | liver cancer | Mutant | 2 |
| BRCA1 | liver cancer | Other | 14 |
| BRCA1 | lung cancer | Mutant | 4 |
| BRCA1 | lung cancer | Other | 65 |
| BRCA1 | lymphoma | Mutant | 1 |
| BRCA1 | lymphoma | Other | 10 |
| BRCA1 | ovarian cancer | Mutant | 3 |
| BRCA1 | ovarian cancer | Other | 32 |
| BRCA1 | pancreatic cancer | Mutant | 1 |
| BRCA1 | pancreatic cancer | Other | 22 |
| BRCA1 | peripheral nervous system neoplasm | Mutant | 1 |
| BRCA1 | peripheral nervous system neoplasm | Other | 12 |
| BRCA1 | skin cancer | Mutant | 2 |
| BRCA1 | skin cancer | Other | 27 |
| BRCA1 | stomach cancer | Mutant | 2 |
| BRCA1 | stomach cancer | Other | 13 |
| BRCA1 | urinary bladder cancer | Mutant | 2 |
| BRCA1 | urinary bladder cancer | Other | 19 |
| BRCA1 | uterine cancer | Mutant | 5 |
| BRCA1 | uterine cancer | Other | 13 |
| EGFR | bone cancer | Mutant | 1 |
| EGFR | bone cancer | Other | 15 |
| EGFR | breast cancer | Mutant | 1 |
| EGFR | breast cancer | Other | 25 |
| EGFR | central nervous system cancer | Mutant | 4 |
| EGFR | central nervous system cancer | Other | 41 |
| EGFR | colorectal cancer | Mutant | 3 |
| EGFR | colorectal cancer | Other | 26 |
| EGFR | esophageal cancer | Mutant | 4 |
| EGFR | esophageal cancer | Other | 11 |
| EGFR | leukemia | Mutant | 2 |
| EGFR | leukemia | Other | 19 |
| EGFR | liver cancer | Mutant | 1 |
| EGFR | liver cancer | Other | 15 |
| EGFR | lung cancer | Mutant | 7 |
| EGFR | lung cancer | Other | 60 |
| EGFR | lymphoma | Mutant | 1 |
| EGFR | lymphoma | Other | 10 |
| EGFR | multiple myeloma | Mutant | 2 |
| EGFR | multiple myeloma | Other | 14 |
| EGFR | ovarian cancer | Mutant | 2 |
| EGFR | ovarian cancer | Other | 33 |
| EGFR | skin cancer | Mutant | 1 |
| EGFR | skin cancer | Other | 28 |
| EGFR | stomach cancer | Mutant | 1 |
| EGFR | stomach cancer | Other | 14 |
| EGFR | uterine cancer | Mutant | 8 |
| EGFR | uterine cancer | Other | 11 |
| PDCD1 | colorectal cancer | Mutant | 1 |
| PDCD1 | colorectal cancer | Other | 26 |
| PDCD1 | lung cancer | Mutant | 2 |
| PDCD1 | lung cancer | Other | 67 |
| PDCD1 | ovarian cancer | Mutant | 1 |
| PDCD1 | ovarian cancer | Other | 34 |
| PDCD1 | uterine cancer | Mutant | 4 |
| PDCD1 | uterine cancer | Other | 14 |
| NPM1 | central nervous system cancer | Mutant | 2 |
| NPM1 | central nervous system cancer | Other | 43 |
| NPM1 | ovarian cancer | Mutant | 1 |
| NPM1 | ovarian cancer | Other | 34 |
| NPM1 | urinary bladder cancer | Mutant | 1 |
| NPM1 | urinary bladder cancer | Other | 20 |
| NPM1 | uterine cancer | Mutant | 1 |
| NPM1 | uterine cancer | Other | 17 |
| MYD88 | bone cancer | Mutant | 1 |
| MYD88 | bone cancer | Other | 15 |
| MYD88 | breast cancer | Mutant | 1 |
| MYD88 | breast cancer | Other | 25 |
| MYD88 | colorectal cancer | Mutant | 1 |
| MYD88 | colorectal cancer | Other | 26 |
| MYD88 | leukemia | Mutant | 1 |
| MYD88 | leukemia | Other | 20 |
| MYD88 | multiple myeloma | Mutant | 1 |
| MYD88 | multiple myeloma | Other | 15 |
| MYD88 | pancreatic cancer | Mutant | 1 |
| MYD88 | pancreatic cancer | Other | 22 |
| MYD88 | urinary bladder cancer | Mutant | 1 |
| MYD88 | urinary bladder cancer | Other | 20 |
| MYD88 | uterine cancer | Mutant | 3 |
| MYD88 | uterine cancer | Other | 15 |
| ROS1 | bone cancer | Mutant | 1 |
| ROS1 | bone cancer | Other | 15 |
| ROS1 | breast cancer | Mutant | 2 |
| ROS1 | breast cancer | Other | 24 |
| ROS1 | cancer | Mutant | 2 |
| ROS1 | cancer | Other | 16 |
| ROS1 | central nervous system cancer | Mutant | 3 |
| ROS1 | central nervous system cancer | Other | 42 |
| ROS1 | colorectal cancer | Mutant | 4 |
| ROS1 | colorectal cancer | Other | 22 |
| ROS1 | esophageal cancer | Mutant | 3 |
| ROS1 | esophageal cancer | Other | 11 |
| ROS1 | head and neck cancer | Mutant | 3 |
| ROS1 | head and neck cancer | Other | 12 |
| ROS1 | kidney cancer | Mutant | 2 |
| ROS1 | kidney cancer | Other | 20 |
| ROS1 | leukemia | Mutant | 1 |
| ROS1 | leukemia | Other | 20 |
| ROS1 | liver cancer | Mutant | 5 |
| ROS1 | liver cancer | Other | 11 |
| ROS1 | lung cancer | Mutant | 3 |
| ROS1 | lung cancer | Other | 66 |
| ROS1 | lymphoma | Mutant | 2 |
| ROS1 | lymphoma | Other | 9 |
| ROS1 | ovarian cancer | Mutant | 1 |
| ROS1 | ovarian cancer | Other | 34 |
| ROS1 | pancreatic cancer | Mutant | 1 |
| ROS1 | pancreatic cancer | Other | 22 |
| ROS1 | peripheral nervous system neoplasm | Mutant | 1 |
| ROS1 | peripheral nervous system neoplasm | Other | 12 |
| ROS1 | skin cancer | Mutant | 5 |
| ROS1 | skin cancer | Other | 25 |
| ROS1 | urinary bladder cancer | Mutant | 1 |
| ROS1 | urinary bladder cancer | Other | 20 |
| ROS1 | uterine cancer | Mutant | 7 |
| ROS1 | uterine cancer | Other | 12 |
ccle_signif_g2p <- compare_means(AUC ~ Mutation_Status_Nonsilent, group.by = "Drug_Gene", data = ccle_data_g2p, method = "wilcox.test", p.adjust.method = "BH")
ccle_signif_g2p <- adj_signif(ccle_signif_g2p)
ccle_signif_g2p <- ccle_signif_g2p[order(ccle_signif_g2p$p),]
saveRDS(ccle_signif_g2p, "./data_munging/rds/ccle_signif_g2p_gene.rds")
ccle_signif_g2p_ByDrug <- lapply(unique(ccle_data_g2p_genesfilt$Drug), WilcoxonByDrug, dataset = ccle_data_g2p_genesfilt, data_name = "ccle")
names(ccle_signif_g2p_ByDrug) <- unique(ccle_data_g2p_genesfilt$Drug)
saveRDS(ccle_signif_g2p_ByDrug, "./data_munging/rds/ccle_signif_g2p_ByDrug.rds")
ccle_signif_g2p <- readRDS("./data_munging/rds/ccle_signif_g2p_gene.rds")
knitr::kable(ccle_signif_g2p[, c("Drug_Gene", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "CCLE: Wilcoxon test results for Level A point mutations, p < 0.01 (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Drug_Gene | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|
| selumetinib_KRAS | 0.0004853 | 0.0043681 | 0.00049 | *** | ** |
| lapatinib_ERBB2 | 0.0500292 | 0.1724797 | 0.05003 | NA | NA |
| nilotinib_UGT1A1 | 0.0574932 | 0.1724797 | 0.05749 | NA | NA |
| erlotinib_MET | 0.1724618 | 0.3880391 | 0.17246 | NA | NA |
| erlotinib_KRAS | 0.3430622 | 0.4860797 | 0.34306 | NA | NA |
| lapatinib_KRAS | 0.3717079 | 0.4860797 | 0.37171 | NA | NA |
| erlotinib_EGFR | 0.3780620 | 0.4860797 | 0.37806 | NA | NA |
| irinotecan_UGT1A1 | 0.8309879 | 0.9348613 | 0.83099 | NA | NA |
| nilotinib_ABL1 | 0.9989982 | 0.9989982 | 0.99900 | NA | NA |
ccle_signif_g2p_ByDrug <- readRDS("./data_munging/rds/ccle_signif_g2p_ByDrug.rds")
ccle_signif_g2p_ByDrug_all <- rbindlist(ccle_signif_g2p_ByDrug, use.names = TRUE)
ccle_signif_g2p_ByDrug_all <- ccle_signif_g2p_ByDrug_all[order(ccle_signif_g2p_ByDrug_all$p),]
knitr::kable(ccle_signif_g2p_ByDrug_all[, c("Hugo_Symbol", "Drug", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "CCLE: by-drug Wilcoxon test results for Level A point mutations, (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | Drug | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|---|
| BRAF | selumetinib | 0.0000000 | 0.0000016 | 4.8e-08 | **** | **** |
| KRAS | selumetinib | 0.0004853 | 0.0082509 | 0.00049 | *** | ** |
| KRAS | irinotecan | 0.0107870 | 0.2265486 | 0.011 |
|
NA |
| ERBB3 | lapatinib | 0.0129696 | 0.4409649 | 0.013 |
|
NA |
| FLT3 | irinotecan | 0.0133264 | 0.2265486 | 0.013 |
|
NA |
| ERBB3 | nilotinib | 0.0219026 | 0.7446883 | 0.022 |
|
NA |
| BRAF | erlotinib | 0.0224018 | 0.4604309 | 0.022 |
|
NA |
| KIT | lapatinib | 0.0299886 | 0.4872398 | 0.030 |
|
NA |
| ERBB2 | erlotinib | 0.0361008 | 0.4604309 | 0.036 |
|
NA |
| PDGFB | erlotinib | 0.0406263 | 0.4604309 | 0.041 |
|
NA |
| TSC2 | irinotecan | 0.0425134 | 0.4818182 | 0.043 |
|
NA |
| ERBB2 | lapatinib | 0.0500292 | 0.4872398 | 0.050 | NA | NA |
| UGT1A1 | nilotinib | 0.0574932 | 0.8315963 | 0.057 | NA | NA |
| ROS1 | lapatinib | 0.0638294 | 0.4872398 | 0.064 | NA | NA |
| JAK2 | irinotecan | 0.0704563 | 0.5988785 | 0.070 | NA | NA |
| MGMT | lapatinib | 0.0716529 | 0.4872398 | 0.072 | NA | NA |
| BRCA2 | selumetinib | 0.0801455 | 0.6177935 | 0.08015 | NA | NA |
| BRAF | nilotinib | 0.0823341 | 0.8315963 | 0.082 | NA | NA |
| G6PD | selumetinib | 0.0848649 | 0.6177935 | 0.08486 | NA | NA |
| DNMT3A | lapatinib | 0.0910216 | 0.4905489 | 0.091 | NA | NA |
| IDH2 | selumetinib | 0.0923191 | 0.6177935 | 0.09232 | NA | NA |
| ROS1 | erlotinib | 0.0964090 | 0.7043128 | 0.096 | NA | NA |
| G6PD | nilotinib | 0.0978349 | 0.8315963 | 0.098 | NA | NA |
| AKT1 | irinotecan | 0.0995560 | 0.6555760 | 0.100 | NA | NA |
| PTCH1 | selumetinib | 0.1105610 | 0.6177935 | 0.11056 | NA | NA |
| BRAF | irinotecan | 0.1223433 | 0.6555760 | 0.122 | NA | NA |
| PDGFRA | selumetinib | 0.1271928 | 0.6177935 | 0.12719 | NA | NA |
| AKT1 | nilotinib | 0.1319214 | 0.8961394 | 0.132 | NA | NA |
| TSC2 | lapatinib | 0.1353477 | 0.4905489 | 0.135 | NA | NA |
| BRCA2 | lapatinib | 0.1454060 | 0.4905489 | 0.145 | NA | NA |
| DNMT3A | selumetinib | 0.1475871 | 0.6272450 | 0.14759 | NA | NA |
| PDGFRA | erlotinib | 0.1494369 | 0.7043128 | 0.149 | NA | NA |
| ERBB3 | erlotinib | 0.1517945 | 0.7043128 | 0.152 | NA | NA |
| PDGFRA | lapatinib | 0.1524894 | 0.4905489 | 0.152 | NA | NA |
| BRAF | lapatinib | 0.1535431 | 0.4905489 | 0.154 | NA | NA |
| MGMT | erlotinib | 0.1554862 | 0.7043128 | 0.155 | NA | NA |
| RET | lapatinib | 0.1587070 | 0.4905489 | 0.159 | NA | NA |
| ESR1 | irinotecan | 0.1628356 | 0.6555760 | 0.163 | NA | NA |
| DPYD | nilotinib | 0.1716871 | 0.8961394 | 0.172 | NA | NA |
| MET | erlotinib | 0.1724618 | 0.7043128 | 0.172 | NA | NA |
| JAK2 | selumetinib | 0.1725059 | 0.6516888 | 0.17251 | NA | NA |
| TPMT | irinotecan | 0.1771488 | 0.6555760 | 0.177 | NA | NA |
| IDH2 | nilotinib | 0.1844993 | 0.8961394 | 0.184 | NA | NA |
| PDGFB | lapatinib | 0.1902003 | 0.5389009 | 0.190 | NA | NA |
| JAK2 | erlotinib | 0.2076226 | 0.7043128 | 0.208 | NA | NA |
| IDH2 | erlotinib | 0.2087321 | 0.7043128 | 0.209 | NA | NA |
| PDGFRB | irinotecan | 0.2131484 | 0.6555760 | 0.213 | NA | NA |
| EGFR | irinotecan | 0.2306603 | 0.6555760 | 0.231 | NA | NA |
| MGMT | irinotecan | 0.2444998 | 0.6555760 | 0.244 | NA | NA |
| ERBB2 | nilotinib | 0.2469369 | 0.9412676 | 0.247 | NA | NA |
| JAK2 | lapatinib | 0.2481605 | 0.6059107 | 0.248 | NA | NA |
| BRCA2 | irinotecan | 0.2519045 | 0.6555760 | 0.252 | NA | NA |
| DPYD | irinotecan | 0.2565617 | 0.6555760 | 0.257 | NA | NA |
| PDGFB | nilotinib | 0.2614178 | 0.9412676 | 0.261 | NA | NA |
| NPM1 | lapatinib | 0.2652151 | 0.6059107 | 0.265 | NA | NA |
| PML | lapatinib | 0.2673135 | 0.6059107 | 0.267 | NA | NA |
| DNMT3A | irinotecan | 0.2699431 | 0.6555760 | 0.270 | NA | NA |
| BRCA2 | erlotinib | 0.2904280 | 0.7043128 | 0.290 | NA | NA |
| KRAS | nilotinib | 0.2905710 | 0.9412676 | 0.291 | NA | NA |
| TSC1 | selumetinib | 0.3026265 | 0.9776385 | 0.30263 | NA | NA |
| PML | erlotinib | 0.3071538 | 0.7043128 | 0.307 | NA | NA |
| RET | selumetinib | 0.3162948 | 0.9776385 | 0.31629 | NA | NA |
| JAK2 | nilotinib | 0.3242397 | 0.9412676 | 0.324 | NA | NA |
| CYP19A1 | irinotecan | 0.3281397 | 0.7321035 | 0.328 | NA | NA |
| KRAS | erlotinib | 0.3430622 | 0.7043128 | 0.343 | NA | NA |
| MET | irinotecan | 0.3595819 | 0.7321035 | 0.360 | NA | NA |
| CYP19A1 | nilotinib | 0.3614358 | 0.9412676 | 0.361 | NA | NA |
| BRCA1 | erlotinib | 0.3656704 | 0.7043128 | 0.366 | NA | NA |
| CYP19A1 | selumetinib | 0.3657355 | 0.9863877 | 0.36574 | NA | NA |
| MYD88 | irinotecan | 0.3660517 | 0.7321035 | 0.366 | NA | NA |
| KRAS | lapatinib | 0.3717079 | 0.7898793 | 0.372 | NA | NA |
| MET | nilotinib | 0.3749787 | 0.9412676 | 0.375 | NA | NA |
| RET | erlotinib | 0.3769409 | 0.7043128 | 0.377 | NA | NA |
| EGFR | erlotinib | 0.3780620 | 0.7043128 | 0.378 | NA | NA |
| KIT | erlotinib | 0.3945572 | 0.7043128 | 0.395 | NA | NA |
| NPM1 | erlotinib | 0.4081068 | 0.7043128 | 0.408 | NA | NA |
| AKT1 | erlotinib | 0.4089836 | 0.7043128 | 0.409 | NA | NA |
| TSC2 | erlotinib | 0.4143017 | 0.7043128 | 0.414 | NA | NA |
| ALK | irinotecan | 0.4159284 | 0.7856426 | 0.416 | NA | NA |
| KIT | selumetinib | 0.4291048 | 0.9863877 | 0.42910 | NA | NA |
| BRCA2 | nilotinib | 0.4329522 | 0.9412676 | 0.433 | NA | NA |
| DNMT3A | nilotinib | 0.4393202 | 0.9412676 | 0.439 | NA | NA |
| ABL1 | lapatinib | 0.4453225 | 0.8186706 | 0.445 | NA | NA |
| FLT3 | erlotinib | 0.4536996 | 0.7345612 | 0.454 | NA | NA |
| ESR1 | selumetinib | 0.4556101 | 0.9863877 | 0.45561 | NA | NA |
| MYD88 | lapatinib | 0.4587151 | 0.8186706 | 0.459 | NA | NA |
| ALK | lapatinib | 0.4609038 | 0.8186706 | 0.461 | NA | NA |
| PDGFRB | nilotinib | 0.4795241 | 0.9412676 | 0.480 | NA | NA |
| ROS1 | irinotecan | 0.4834670 | 0.8355783 | 0.483 | NA | NA |
| TPMT | erlotinib | 0.4842070 | 0.7483199 | 0.484 | NA | NA |
| DPYD | lapatinib | 0.4951753 | 0.8186706 | 0.495 | NA | NA |
| PDGFB | irinotecan | 0.5117862 | 0.8355783 | 0.512 | NA | NA |
| ESR1 | nilotinib | 0.5209092 | 0.9412676 | 0.521 | NA | NA |
| NPM1 | nilotinib | 0.5225901 | 0.9412676 | 0.523 | NA | NA |
| BRCA1 | lapatinib | 0.5346294 | 0.8186706 | 0.535 | NA | NA |
| IDH2 | irinotecan | 0.5383687 | 0.8355783 | 0.538 | NA | NA |
| ESR1 | erlotinib | 0.5463206 | 0.8076043 | 0.546 | NA | NA |
| MET | lapatinib | 0.5678884 | 0.8186706 | 0.568 | NA | NA |
| CYP19A1 | erlotinib | 0.5725012 | 0.8110433 | 0.573 | NA | NA |
| EGFR | selumetinib | 0.5763443 | 0.9863877 | 0.57634 | NA | NA |
| PDGFRB | lapatinib | 0.5810825 | 0.8186706 | 0.581 | NA | NA |
| UGT1A1 | lapatinib | 0.5880643 | 0.8186706 | 0.588 | NA | NA |
| FLT3 | nilotinib | 0.5913464 | 0.9412676 | 0.591 | NA | NA |
| PDGFRA | irinotecan | 0.5925752 | 0.8355783 | 0.593 | NA | NA |
| RET | nilotinib | 0.5975829 | 0.9412676 | 0.598 | NA | NA |
| TSC1 | irinotecan | 0.6014923 | 0.8355783 | 0.601 | NA | NA |
| AKT1 | lapatinib | 0.6019637 | 0.8186706 | 0.602 | NA | NA |
| TSC2 | selumetinib | 0.6111574 | 0.9863877 | 0.61116 | NA | NA |
| ERBB2 | irinotecan | 0.6286426 | 0.8355783 | 0.629 | NA | NA |
| PML | irinotecan | 0.6294330 | 0.8355783 | 0.629 | NA | NA |
| G6PD | lapatinib | 0.6332410 | 0.8280844 | 0.633 | NA | NA |
| RET | irinotecan | 0.6389716 | 0.8355783 | 0.639 | NA | NA |
| TSC1 | erlotinib | 0.6505989 | 0.8848145 | 0.651 | NA | NA |
| MET | selumetinib | 0.6524774 | 0.9863877 | 0.65248 | NA | NA |
| KIT | nilotinib | 0.6606331 | 0.9412676 | 0.661 | NA | NA |
| ABL1 | selumetinib | 0.6628862 | 0.9863877 | 0.66289 | NA | NA |
| PDGFRB | selumetinib | 0.6645199 | 0.9863877 | 0.66452 | NA | NA |
| ABL1 | irinotecan | 0.6660281 | 0.8387021 | 0.666 | NA | NA |
| TPMT | nilotinib | 0.6679929 | 0.9412676 | 0.668 | NA | NA |
| ROS1 | nilotinib | 0.6819122 | 0.9412676 | 0.682 | NA | NA |
| DPYD | erlotinib | 0.6840148 | 0.8944809 | 0.684 | NA | NA |
| DPYD | selumetinib | 0.6868738 | 0.9863877 | 0.68687 | NA | NA |
| MYD88 | nilotinib | 0.6912056 | 0.9412676 | 0.691 | NA | NA |
| TSC2 | nilotinib | 0.6921085 | 0.9412676 | 0.692 | NA | NA |
| CYP19A1 | lapatinib | 0.6950890 | 0.8752973 | 0.695 | NA | NA |
| PTCH1 | irinotecan | 0.7162618 | 0.8697465 | 0.716 | NA | NA |
| MYD88 | selumetinib | 0.7246756 | 0.9863877 | 0.72468 | NA | NA |
| PTCH1 | erlotinib | 0.7302464 | 0.9195695 | 0.730 | NA | NA |
| TSC1 | lapatinib | 0.7401698 | 0.8933363 | 0.740 | NA | NA |
| PDGFB | selumetinib | 0.7634636 | 0.9863877 | 0.76346 | NA | NA |
| G6PD | erlotinib | 0.7787902 | 0.9278477 | 0.779 | NA | NA |
| PTCH1 | lapatinib | 0.7871784 | 0.8933363 | 0.787 | NA | NA |
| EGFR | lapatinib | 0.7947247 | 0.8933363 | 0.795 | NA | NA |
| ALK | nilotinib | 0.7983903 | 0.9829706 | 0.798 | NA | NA |
| TSC1 | nilotinib | 0.7988924 | 0.9829706 | 0.799 | NA | NA |
| IDH2 | lapatinib | 0.8145125 | 0.8933363 | 0.815 | NA | NA |
| BRCA1 | irinotecan | 0.8210965 | 0.9114060 | 0.821 | NA | NA |
| ERBB2 | selumetinib | 0.8218228 | 0.9863877 | 0.82182 | NA | NA |
| UGT1A1 | erlotinib | 0.8238031 | 0.9278477 | 0.824 | NA | NA |
| G6PD | irinotecan | 0.8254252 | 0.9114060 | 0.825 | NA | NA |
| ROS1 | selumetinib | 0.8271911 | 0.9863877 | 0.82719 | NA | NA |
| ALK | selumetinib | 0.8278795 | 0.9863877 | 0.82788 | NA | NA |
| PDGFRB | erlotinib | 0.8279937 | 0.9278477 | 0.828 | NA | NA |
| MGMT | nilotinib | 0.8301945 | 0.9829706 | 0.830 | NA | NA |
| UGT1A1 | irinotecan | 0.8309879 | 0.9114060 | 0.831 | NA | NA |
| ABL1 | erlotinib | 0.8522490 | 0.9278477 | 0.852 | NA | NA |
| FLT3 | selumetinib | 0.8527746 | 0.9863877 | 0.85277 | NA | NA |
| FLT3 | lapatinib | 0.8614733 | 0.9153153 | 0.861 | NA | NA |
| PDGFRA | nilotinib | 0.8621321 | 0.9829706 | 0.862 | NA | NA |
| ERBB3 | selumetinib | 0.8669447 | 0.9863877 | 0.86694 | NA | NA |
| NPM1 | selumetinib | 0.8832243 | 0.9863877 | 0.88322 | NA | NA |
| KIT | irinotecan | 0.8862231 | 0.9200633 | 0.886 | NA | NA |
| MYD88 | erlotinib | 0.8885739 | 0.9278477 | 0.889 | NA | NA |
| UGT1A1 | selumetinib | 0.8917738 | 0.9863877 | 0.89177 | NA | NA |
| NPM1 | irinotecan | 0.8930026 | 0.9200633 | 0.893 | NA | NA |
| DNMT3A | erlotinib | 0.9005581 | 0.9278477 | 0.901 | NA | NA |
| TPMT | lapatinib | 0.9089736 | 0.9365183 | 0.909 | NA | NA |
| PML | nilotinib | 0.9170484 | 0.9829706 | 0.917 | NA | NA |
| AKT1 | selumetinib | 0.9187209 | 0.9863877 | 0.91872 | NA | NA |
| MGMT | selumetinib | 0.9254057 | 0.9863877 | 0.92541 | NA | NA |
| ALK | erlotinib | 0.9492432 | 0.9492432 | 0.949 | NA | NA |
| PML | selumetinib | 0.9504098 | 0.9863877 | 0.95041 | NA | NA |
| BRCA1 | nilotinib | 0.9506540 | 0.9829706 | 0.951 | NA | NA |
| PTCH1 | nilotinib | 0.9525059 | 0.9829706 | 0.953 | NA | NA |
| EGFR | nilotinib | 0.9540597 | 0.9829706 | 0.954 | NA | NA |
| BRCA1 | selumetinib | 0.9592240 | 0.9863877 | 0.95922 | NA | NA |
| ESR1 | lapatinib | 0.9641363 | 0.9641363 | 0.964 | NA | NA |
| ERBB3 | irinotecan | 0.9705439 | 0.9705439 | 0.971 | NA | NA |
| TPMT | selumetinib | 0.9863877 | 0.9863877 | 0.98639 | NA | NA |
| ABL1 | nilotinib | 0.9989982 | 0.9989982 | 0.999 | NA | NA |
ctrp_signif_g2p <- compare_means(AUC ~ Mutation_Status_Nonsilent, group.by = "Drug_Gene", data = ctrp_data_g2p, method = "wilcox.test", p.adjust.method = "BH")
ctrp_signif_g2p <- adj_signif(ctrp_signif_g2p)
ctrp_signif_g2p <- ctrp_signif_g2p[order(ctrp_signif_g2p$p),]
saveRDS(ctrp_signif_g2p, "./data_munging/rds/ctrp_signif_g2p_gene.rds")
ctrp_signif_g2p_ByDrug <- lapply(unique(ctrp_data_g2p_genesfilt$Drug), WilcoxonByDrug, dataset = ctrp_data_g2p_genesfilt, data_name = "CTRP")
names(ctrp_signif_g2p_ByDrug) <- unique(ctrp_data_g2p_genesfilt$Drug)
saveRDS(ctrp_signif_g2p_ByDrug, "./data_munging/rds/ctrp_signif_g2p_ByDrug.rds")
ctrp_signif_g2p <- readRDS("./data_munging/rds/ctrp_signif_g2p_gene.rds")
knitr::kable(ctrp_signif_g2p[, c("Drug_Gene", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "CTRP: Wilcoxon test results for Level A point mutations, p < 0.01 (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Drug_Gene | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|
| vemurafenib_BRAF | 0.0000005 | 0.0000236 | 4.9e-07 | **** | **** |
| lapatinib_KRAS | 0.0000056 | 0.0001343 | 5.6e-06 | **** | *** |
| selumetinib_KRAS | 0.0002012 | 0.0032190 | 0.00020 | *** | ** |
| dabrafenib_BRAF | 0.0002722 | 0.0032664 | 0.00027 | *** | ** |
| gefitinib_KRAS | 0.0040210 | 0.0386011 | 0.00402 | ** |
|
| imatinib_PDGFRB | 0.0054451 | 0.0435604 | 0.00545 | ** |
|
| trametinib_BRAF | 0.0064941 | 0.0445309 | 0.00649 | ** |
|
| cyclophosphamide_ERBB2 | 0.0089622 | 0.0537731 | 0.00896 | ** | NA |
| afatinib_KRAS | 0.0107829 | 0.0575089 | 0.01078 |
|
NA |
| azd_KRAS | 0.0127676 | 0.0612847 | 0.01277 |
|
NA |
| pazopanib_UGT1A1 | 0.0341719 | 0.1491138 | 0.03417 |
|
NA |
| crizotinib_MET | 0.0436200 | 0.1744801 | 0.04362 |
|
NA |
| crizotinib_ALK | 0.0595488 | 0.2048823 | 0.05955 | NA | NA |
| fulvestrant_ERBB2 | 0.0667862 | 0.2048823 | 0.06679 | NA | NA |
| crizotinib_ROS1 | 0.0682314 | 0.2048823 | 0.06823 | NA | NA |
| gefitinib_MET | 0.0682941 | 0.2048823 | 0.06829 | NA | NA |
| dabrafenib_G6PD | 0.0952173 | 0.2688489 | 0.09522 | NA | NA |
| sunitinib_PDGFRA | 0.1625269 | 0.4059909 | 0.16253 | NA | NA |
| temozolomide_MGMT | 0.1678755 | 0.4059909 | 0.16788 | NA | NA |
| vandetanib_RET | 0.1691629 | 0.4059909 | 0.16916 | NA | NA |
| afatinib_ERBB2 | 0.1962848 | 0.4486509 | 0.19628 | NA | NA |
| neratinib_ERBB2 | 0.2066706 | 0.4509176 | 0.20667 | NA | NA |
| azd_EGFR | 0.2197291 | 0.4585650 | 0.21973 | NA | NA |
| afatinib_EGFR | 0.2518397 | 0.5036794 | 0.25184 | NA | NA |
| ibrutinib_MYD88 | 0.3177454 | 0.5850208 | 0.31775 | NA | NA |
| regorafenib_PDGFRA | 0.3247031 | 0.5850208 | 0.32470 | NA | NA |
| imatinib_PDGFB | 0.3290742 | 0.5850208 | 0.32907 | NA | NA |
| regorafenib_KIT | 0.4759780 | 0.8159623 | 0.47598 | NA | NA |
| olaparib_BRCA2 | 0.5281161 | 0.8473422 | 0.52812 | NA | NA |
| sunitinib_KIT | 0.5322976 | 0.8473422 | 0.53230 | NA | NA |
| erlotinib_EGFR | 0.5472418 | 0.8473422 | 0.54724 | NA | NA |
| imatinib_ABL1 | 0.5818558 | 0.8613135 | 0.58186 | NA | NA |
| cabozantinib_RET | 0.6089852 | 0.8613135 | 0.60899 | NA | NA |
| nilotinib_ABL1 | 0.6182260 | 0.8613135 | 0.61823 | NA | NA |
| imatinib_KIT | 0.6429646 | 0.8613135 | 0.64296 | NA | NA |
| erlotinib_MET | 0.6459851 | 0.8613135 | 0.64599 | NA | NA |
| fulvestrant_ESR1 | 0.6748204 | 0.8754427 | 0.67482 | NA | NA |
| afatinib_ERBB3 | 0.6959010 | 0.8790329 | 0.69590 | NA | NA |
| nilotinib_UGT1A1 | 0.7429748 | 0.8953061 | 0.74297 | NA | NA |
| fluorouracil_DPYD | 0.7693491 | 0.8953061 | 0.76935 | NA | NA |
| dasatinib_ABL1 | 0.7801253 | 0.8953061 | 0.78013 | NA | NA |
| olaparib_BRCA1 | 0.8126710 | 0.8953061 | 0.81267 | NA | NA |
| erlotinib_KRAS | 0.8197849 | 0.8953061 | 0.81978 | NA | NA |
| ruxolitinib_JAK2 | 0.8206972 | 0.8953061 | 0.82070 | NA | NA |
| imatinib_PDGFRA | 0.8550665 | 0.9120709 | 0.85507 | NA | NA |
| gefitinib_EGFR | 0.8875800 | 0.9156890 | 0.88758 | NA | NA |
| lapatinib_ERBB2 | 0.8966122 | 0.9156890 | 0.89661 | NA | NA |
| belinostat_UGT1A1 | 0.9223455 | 0.9223455 | 0.92235 | NA | NA |
ctrp_signif_g2p_ByDrug <- readRDS("./data_munging/rds/ctrp_signif_g2p_ByDrug.rds")
ctrp_signif_g2p_ByDrug_all <- rbindlist(ctrp_signif_g2p_ByDrug, use.names = TRUE)
ctrp_signif_g2p_ByDrug_all <- ctrp_signif_g2p_ByDrug_all[order(ctrp_signif_g2p_ByDrug_all$p),]
knitr::kable(ctrp_signif_g2p_ByDrug_all[, c("Hugo_Symbol", "Drug", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "CTRP: by-drug Wilcoxon test results for Level A point mutations, (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | Drug | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|---|
| BRAF | vemurafenib | 0.0000005 | 0.0000167 | 4.9e-07 | **** | **** |
| KRAS | lapatinib | 0.0000056 | 0.0001902 | 5.6e-06 | **** | *** |
| KRAS | trametinib | 0.0000123 | 0.0004073 | 1.2e-05 | **** | *** |
| KRAS | pazopanib | 0.0000172 | 0.0005849 | 1.7e-05 | **** | *** |
| KRAS | ibrutinib | 0.0000293 | 0.0009955 | 2.9e-05 | **** | *** |
| MYD88 | vemurafenib | 0.0000321 | 0.0005454 | 3.2e-05 | **** | *** |
| KRAS | selumetinib | 0.0002012 | 0.0035372 | 0.00020 | *** | ** |
| BRAF | selumetinib | 0.0002081 | 0.0035372 | 0.00021 | *** | ** |
| BRAF | olaparib | 0.0002505 | 0.0085179 | 0.00025 | *** | ** |
| BRAF | dabrafenib | 0.0002722 | 0.0089827 | 0.00027 | *** | ** |
| KRAS | sunitinib | 0.0004277 | 0.0145425 | 0.00043 | *** |
|
| KRAS | neratinib | 0.0004366 | 0.0148460 | 0.00044 | *** |
|
| EGFR | vemurafenib | 0.0006405 | 0.0072593 | 0.00064 | *** | ** |
| BRAF | afatinib | 0.0008985 | 0.0305482 | 0.0009 | *** |
|
| KRAS | vandetanib | 0.0012628 | 0.0296819 | 0.0013 | ** |
|
| DNMT3A | vandetanib | 0.0017460 | 0.0296819 | 0.0017 | ** |
|
| KRAS | cabozantinib | 0.0020791 | 0.0706877 | 0.0021 | ** | NA |
| DNMT3A | lapatinib | 0.0028992 | 0.0492861 | 0.0029 | ** |
|
| CYP19A1 | vemurafenib | 0.0034645 | 0.0294485 | 0.00346 | ** |
|
| KRAS | olaparib | 0.0035982 | 0.0611698 | 0.00360 | ** | NA |
| KRAS | gefitinib | 0.0040210 | 0.1367124 | 0.004 | ** | NA |
| BRAF | neratinib | 0.0041088 | 0.0698503 | 0.00411 | ** | NA |
| BRAF | pazopanib | 0.0041184 | 0.0700128 | 0.0041 | ** | NA |
| BRAF | ibrutinib | 0.0051142 | 0.0869422 | 0.0051 | ** | NA |
| DNMT3A | selumetinib | 0.0054340 | 0.0615849 | 0.00543 | ** | NA |
| PDGFRB | imatinib | 0.0054451 | 0.1851319 | 0.0054 | ** | NA |
| PML | fulvestrant | 0.0061906 | 0.2104795 | 0.0062 | ** | NA |
| BRAF | ruxolitinib | 0.0062716 | 0.2132360 | 0.0063 | ** | NA |
| PDGFRB | cabozantinib | 0.0062762 | 0.1066960 | 0.0063 | ** | NA |
| BRAF | trametinib | 0.0064941 | 0.1071526 | 0.0065 | ** | NA |
| DNMT3A | gefitinib | 0.0080435 | 0.1367399 | 0.008 | ** | NA |
| ERBB2 | cyclophosphamide | 0.0089622 | 0.3047143 | 0.009 | ** | NA |
| KRAS | regorafenib | 0.0098050 | 0.1882113 | 0.0098 | ** | NA |
| ERBB2 | cabozantinib | 0.0100336 | 0.1091138 | 0.0100 |
|
NA |
| KRAS | afatinib | 0.0107829 | 0.1699989 | 0.0108 |
|
NA |
| PML | crizotinib | 0.0111785 | 0.3800698 | 0.011 |
|
NA |
| KRAS | vemurafenib | 0.0119766 | 0.0814412 | 0.01198 |
|
NA |
| MYD88 | vandetanib | 0.0123446 | 0.1399058 | 0.0123 |
|
NA |
| KRAS | azd | 0.0127676 | 0.2040480 | 0.013 |
|
NA |
| ERBB3 | cabozantinib | 0.0128369 | 0.1091138 | 0.0128 |
|
NA |
| BRAF | temozolomide | 0.0137195 | 0.4000874 | 0.014 |
|
NA |
| KIT | ibrutinib | 0.0142737 | 0.1617685 | 0.0143 |
|
NA |
| TPMT | sunitinib | 0.0149004 | 0.2533066 | 0.01490 |
|
NA |
| DNMT3A | afatinib | 0.0149999 | 0.1699989 | 0.0150 |
|
NA |
| PML | fluorouracil | 0.0155734 | 0.5294946 | 0.016 |
|
NA |
| RET | azd | 0.0156276 | 0.2040480 | 0.016 |
|
NA |
| PTCH1 | trametinib | 0.0159153 | 0.1750680 | 0.0159 |
|
NA |
| ROS1 | pazopanib | 0.0165094 | 0.1871070 | 0.0165 |
|
NA |
| PDGFB | regorafenib | 0.0165670 | 0.1882113 | 0.0166 |
|
NA |
| CYP19A1 | regorafenib | 0.0166069 | 0.1882113 | 0.0166 |
|
NA |
| UGT1A1 | azd | 0.0180042 | 0.2040480 | 0.018 |
|
NA |
| BRAF | cyclophosphamide | 0.0222337 | 0.3779730 | 0.022 |
|
NA |
| ALK | neratinib | 0.0230681 | 0.2614389 | 0.02307 |
|
NA |
| DNMT3A | trametinib | 0.0232930 | 0.1921671 | 0.0233 |
|
NA |
| ESR1 | imatinib | 0.0245120 | 0.4167035 | 0.0245 |
|
NA |
| BRCA1 | fulvestrant | 0.0266668 | 0.4533360 | 0.0267 |
|
NA |
| JAK2 | temozolomide | 0.0271063 | 0.4000874 | 0.027 |
|
NA |
| DNMT3A | crizotinib | 0.0276455 | 0.3866447 | 0.028 |
|
NA |
| BRAF | dasatinib | 0.0300319 | 0.7302743 | 0.030 |
|
NA |
| BRAF | lapatinib | 0.0305016 | 0.3456843 | 0.0305 |
|
NA |
| PML | selumetinib | 0.0317252 | 0.2169061 | 0.03173 |
|
NA |
| PDGFRA | ibrutinib | 0.0333483 | 0.2315548 | 0.0333 |
|
NA |
| DNMT3A | ibrutinib | 0.0340522 | 0.2315548 | 0.0341 |
|
NA |
| UGT1A1 | pazopanib | 0.0341719 | 0.2904612 | 0.0342 |
|
NA |
| TSC2 | vemurafenib | 0.0345796 | 0.1751927 | 0.03458 |
|
NA |
| DPYD | selumetinib | 0.0356352 | 0.2169061 | 0.03564 |
|
NA |
| DNMT3A | neratinib | 0.0356380 | 0.3029234 | 0.03564 |
|
NA |
| MET | vemurafenib | 0.0360691 | 0.1751927 | 0.03607 |
|
NA |
| KIT | cabozantinib | 0.0362427 | 0.1752370 | 0.0362 |
|
NA |
| PDGFRB | afatinib | 0.0366997 | 0.2708095 | 0.0367 |
|
NA |
| ROS1 | gefitinib | 0.0380067 | 0.3938390 | 0.038 |
|
NA |
| TPMT | selumetinib | 0.0382776 | 0.2169061 | 0.03828 |
|
NA |
| TSC2 | cabozantinib | 0.0383320 | 0.1752370 | 0.0383 |
|
NA |
| ROS1 | cabozantinib | 0.0390533 | 0.1752370 | 0.0391 |
|
NA |
| BRAF | fluorouracil | 0.0393299 | 0.5857145 | 0.039 |
|
NA |
| KIT | afatinib | 0.0398249 | 0.2708095 | 0.0398 |
|
NA |
| FLT3 | cabozantinib | 0.0412322 | 0.1752370 | 0.0412 |
|
NA |
| MET | sunitinib | 0.0414057 | 0.3813132 | 0.04141 |
|
NA |
| BRAF | azd | 0.0415725 | 0.3045006 | 0.042 |
|
NA |
| DNMT3A | erlotinib | 0.0426319 | 0.4945308 | 0.043 |
|
NA |
| CYP19A1 | imatinib | 0.0430959 | 0.4184794 | 0.0431 |
|
NA |
| FLT3 | olaparib | 0.0434999 | 0.3890797 | 0.04350 |
|
NA |
| MET | crizotinib | 0.0436200 | 0.3866447 | 0.044 |
|
NA |
| ROS1 | azd | 0.0447795 | 0.3045006 | 0.045 |
|
NA |
| ROS1 | olaparib | 0.0457741 | 0.3890797 | 0.04577 |
|
NA |
| TSC1 | nilotinib | 0.0489600 | 0.4507292 | 0.049 |
|
NA |
| BRCA1 | belinostat | 0.0497327 | 0.9332615 | 0.05 |
|
NA |
| PDGFRB | regorafenib | 0.0500392 | 0.3550591 | 0.0500 | NA | NA |
| ALK | dasatinib | 0.0501428 | 0.7302743 | 0.050 | NA | NA |
| MET | selumetinib | 0.0507587 | 0.2252140 | 0.05076 | NA | NA |
| KRAS | crizotinib | 0.0508005 | 0.3866447 | 0.051 | NA | NA |
| PTCH1 | regorafenib | 0.0522146 | 0.3550591 | 0.0522 | NA | NA |
| PTCH1 | vemurafenib | 0.0527029 | 0.2006954 | 0.05270 | NA | NA |
| RET | selumetinib | 0.0529915 | 0.2252140 | 0.05299 | NA | NA |
| BRCA1 | vemurafenib | 0.0531252 | 0.2006954 | 0.05313 | NA | NA |
| ALK | vandetanib | 0.0531880 | 0.4520980 | 0.0532 | NA | NA |
| PDGFRA | gefitinib | 0.0538638 | 0.3938390 | 0.054 | NA | NA |
| MET | nilotinib | 0.0553000 | 0.4507292 | 0.055 | NA | NA |
| JAK2 | nilotinib | 0.0558396 | 0.4507292 | 0.056 | NA | NA |
| TPMT | imatinib | 0.0564058 | 0.4184794 | 0.0564 | NA | NA |
| BRCA2 | temozolomide | 0.0567584 | 0.4000874 | 0.057 | NA | NA |
| MYD88 | temozolomide | 0.0574402 | 0.4000874 | 0.057 | NA | NA |
| NPM1 | lapatinib | 0.0576027 | 0.4247950 | 0.0576 | NA | NA |
| MGMT | dabrafenib | 0.0578528 | 0.6995857 | 0.05785 | NA | NA |
| IDH2 | olaparib | 0.0581368 | 0.3953299 | 0.05814 | NA | NA |
| PTCH1 | temozolomide | 0.0588364 | 0.4000874 | 0.059 | NA | NA |
| ALK | crizotinib | 0.0595488 | 0.3866447 | 0.060 | NA | NA |
| JAK2 | cabozantinib | 0.0601835 | 0.1902348 | 0.0602 | NA | NA |
| ABL1 | cyclophosphamide | 0.0608027 | 0.6890967 | 0.061 | NA | NA |
| PDGFRB | sunitinib | 0.0609026 | 0.3813132 | 0.06090 | NA | NA |
| PTCH1 | imatinib | 0.0615411 | 0.4184794 | 0.0615 | NA | NA |
| DPYD | neratinib | 0.0622681 | 0.4234232 | 0.06227 | NA | NA |
| PDGFRA | lapatinib | 0.0624698 | 0.4247950 | 0.0625 | NA | NA |
| PTCH1 | erlotinib | 0.0624883 | 0.4945308 | 0.062 | NA | NA |
| MET | cabozantinib | 0.0628214 | 0.1902348 | 0.0628 | NA | NA |
| CYP19A1 | dasatinib | 0.0644360 | 0.7302743 | 0.064 | NA | NA |
| PTCH1 | sunitinib | 0.0653514 | 0.3813132 | 0.06535 | NA | NA |
| UGT1A1 | cabozantinib | 0.0659861 | 0.1902348 | 0.0660 | NA | NA |
| ERBB2 | fulvestrant | 0.0667862 | 0.7405746 | 0.0668 | NA | NA |
| AKT1 | cabozantinib | 0.0671417 | 0.1902348 | 0.0671 | NA | NA |
| DNMT3A | sunitinib | 0.0672906 | 0.3813132 | 0.06729 | NA | NA |
| EGFR | regorafenib | 0.0674563 | 0.3598309 | 0.0675 | NA | NA |
| ROS1 | crizotinib | 0.0682314 | 0.3866447 | 0.068 | NA | NA |
| MET | gefitinib | 0.0682941 | 0.3938390 | 0.068 | NA | NA |
| ROS1 | erlotinib | 0.0687863 | 0.4945308 | 0.069 | NA | NA |
| JAK2 | erlotinib | 0.0694206 | 0.4945308 | 0.069 | NA | NA |
| JAK2 | gefitinib | 0.0695010 | 0.3938390 | 0.070 | NA | NA |
| KRAS | ruxolitinib | 0.0698118 | 0.9314078 | 0.0698 | NA | NA |
| KRAS | nilotinib | 0.0700538 | 0.4507292 | 0.070 | NA | NA |
| TPMT | afatinib | 0.0710783 | 0.3521922 | 0.0711 | NA | NA |
| DPYD | azd | 0.0712184 | 0.4035707 | 0.071 | NA | NA |
| ALK | afatinib | 0.0725102 | 0.3521922 | 0.0725 | NA | NA |
| PDGFRA | vemurafenib | 0.0735826 | 0.2190817 | 0.07358 | NA | NA |
| G6PD | regorafenib | 0.0740828 | 0.3598309 | 0.0741 | NA | NA |
| KIT | selumetinib | 0.0746874 | 0.2821523 | 0.07469 | NA | NA |
| NPM1 | pazopanib | 0.0750765 | 0.5105199 | 0.0751 | NA | NA |
| TPMT | cabozantinib | 0.0751475 | 0.1965396 | 0.0751 | NA | NA |
| TSC1 | vemurafenib | 0.0759962 | 0.2190817 | 0.07600 | NA | NA |
| PML | vemurafenib | 0.0789218 | 0.2190817 | 0.07892 | NA | NA |
| TSC1 | fluorouracil | 0.0794633 | 0.5857145 | 0.079 | NA | NA |
| UGT1A1 | sunitinib | 0.0800633 | 0.3888788 | 0.08006 | NA | NA |
| DNMT3A | fluorouracil | 0.0810167 | 0.5857145 | 0.081 | NA | NA |
| G6PD | nilotinib | 0.0817599 | 0.4507292 | 0.082 | NA | NA |
| PDGFRA | erlotinib | 0.0818940 | 0.4945308 | 0.082 | NA | NA |
| ERBB2 | dabrafenib | 0.0822127 | 0.6995857 | 0.08221 | NA | NA |
| RET | afatinib | 0.0832455 | 0.3537932 | 0.0832 | NA | NA |
| PDGFRB | trametinib | 0.0837396 | 0.4658024 | 0.0837 | NA | NA |
| BRCA2 | vemurafenib | 0.0837665 | 0.2190817 | 0.08377 | NA | NA |
| MYD88 | nilotinib | 0.0840035 | 0.4507292 | 0.084 | NA | NA |
| BRCA1 | azd | 0.0871239 | 0.4231730 | 0.087 | NA | NA |
| TPMT | crizotinib | 0.0889926 | 0.4322498 | 0.089 | NA | NA |
| KIT | trametinib | 0.0892804 | 0.4658024 | 0.0893 | NA | NA |
| RET | fluorouracil | 0.0904485 | 0.5857145 | 0.090 | NA | NA |
| BRCA2 | pazopanib | 0.0923309 | 0.5232086 | 0.0923 | NA | NA |
| TPMT | dasatinib | 0.0925509 | 0.7866823 | 0.093 | NA | NA |
| ROS1 | nilotinib | 0.0927972 | 0.4507292 | 0.093 | NA | NA |
| PDGFRA | temozolomide | 0.0937160 | 0.5310575 | 0.094 | NA | NA |
| G6PD | dabrafenib | 0.0952173 | 0.6995857 | 0.09522 | NA | NA |
| RET | cyclophosphamide | 0.0968718 | 0.8234099 | 0.097 | NA | NA |
| DNMT3A | olaparib | 0.0996068 | 0.5644383 | 0.09961 | NA | NA |
| DPYD | afatinib | 0.1034804 | 0.3909259 | 0.1035 | NA | NA |
| ABL1 | trametinib | 0.1038508 | 0.4658024 | 0.1039 | NA | NA |
| MGMT | imatinib | 0.1047274 | 0.5934553 | 0.1047 | NA | NA |
| DPYD | vandetanib | 0.1050806 | 0.6681475 | 0.1051 | NA | NA |
| PDGFB | ibrutinib | 0.1088089 | 0.5415524 | 0.1088 | NA | NA |
| MGMT | erlotinib | 0.1093037 | 0.4945308 | 0.109 | NA | NA |
| AKT1 | crizotinib | 0.1095589 | 0.4656252 | 0.110 | NA | NA |
| AKT1 | azd | 0.1125486 | 0.4576031 | 0.113 | NA | NA |
| RET | trametinib | 0.1129218 | 0.4658024 | 0.1129 | NA | NA |
| UGT1A1 | dabrafenib | 0.1142522 | 0.6995857 | 0.11425 | NA | NA |
| ESR1 | fluorouracil | 0.1147435 | 0.5857145 | 0.115 | NA | NA |
| DNMT3A | pazopanib | 0.1153640 | 0.5603392 | 0.1154 | NA | NA |
| PDGFB | vemurafenib | 0.1163543 | 0.2825748 | 0.11635 | NA | NA |
| PTCH1 | lapatinib | 0.1167103 | 0.6029902 | 0.1167 | NA | NA |
| AKT1 | sunitinib | 0.1198936 | 0.4988051 | 0.11989 | NA | NA |
| PDGFRA | azd | 0.1211302 | 0.4576031 | 0.121 | NA | NA |
| BRCA1 | nilotinib | 0.1242641 | 0.4564231 | 0.124 | NA | NA |
| TPMT | neratinib | 0.1244008 | 0.6384596 | 0.12440 | NA | NA |
| TSC1 | cabozantinib | 0.1252422 | 0.3041597 | 0.1252 | NA | NA |
| PML | gefitinib | 0.1255530 | 0.6098289 | 0.126 | NA | NA |
| ERBB2 | fluorouracil | 0.1257464 | 0.5857145 | 0.126 | NA | NA |
| CYP19A1 | ibrutinib | 0.1269984 | 0.5415524 | 0.1270 | NA | NA |
| CYP19A1 | dabrafenib | 0.1271974 | 0.6995857 | 0.12720 | NA | NA |
| ALK | ibrutinib | 0.1274241 | 0.5415524 | 0.1274 | NA | NA |
| PTCH1 | nilotinib | 0.1277181 | 0.4564231 | 0.128 | NA | NA |
| NPM1 | erlotinib | 0.1307567 | 0.4945308 | 0.131 | NA | NA |
| EGFR | trametinib | 0.1316155 | 0.4825901 | 0.1316 | NA | NA |
| NPM1 | sunitinib | 0.1320366 | 0.4988051 | 0.13204 | NA | NA |
| ROS1 | regorafenib | 0.1323222 | 0.5623696 | 0.1323 | NA | NA |
| JAK2 | vemurafenib | 0.1329072 | 0.3012562 | 0.13291 | NA | NA |
| BRAF | imatinib | 0.1350841 | 0.6561226 | 0.1351 | NA | NA |
| BRCA2 | neratinib | 0.1369451 | 0.6384596 | 0.13695 | NA | NA |
| PTCH1 | olaparib | 0.1376429 | 0.6685514 | 0.13764 | NA | NA |
| TPMT | ruxolitinib | 0.1408874 | 0.9314078 | 0.1409 | NA | NA |
| UGT1A1 | selumetinib | 0.1423368 | 0.4163122 | 0.14234 | NA | NA |
| MGMT | fluorouracil | 0.1432551 | 0.5857145 | 0.143 | NA | NA |
| BRCA2 | erlotinib | 0.1458082 | 0.4945308 | 0.146 | NA | NA |
| ALK | erlotinib | 0.1462901 | 0.4945308 | 0.146 | NA | NA |
| FLT3 | nilotinib | 0.1476259 | 0.4564231 | 0.148 | NA | NA |
| DPYD | nilotinib | 0.1476663 | 0.4564231 | 0.148 | NA | NA |
| G6PD | trametinib | 0.1496537 | 0.4938571 | 0.1497 | NA | NA |
| TSC1 | sunitinib | 0.1518085 | 0.5023558 | 0.15181 | NA | NA |
| AKT1 | neratinib | 0.1528627 | 0.6384596 | 0.15286 | NA | NA |
| DPYD | fulvestrant | 0.1532097 | 0.7405746 | 0.1532 | NA | NA |
| ERBB2 | erlotinib | 0.1533325 | 0.4945308 | 0.153 | NA | NA |
| G6PD | selumetinib | 0.1551003 | 0.4163122 | 0.15510 | NA | NA |
| PDGFRB | selumetinib | 0.1562725 | 0.4163122 | 0.15627 | NA | NA |
| ALK | azd | 0.1572449 | 0.5346326 | 0.157 | NA | NA |
| FLT3 | vemurafenib | 0.1577275 | 0.3259020 | 0.15773 | NA | NA |
| NPM1 | crizotinib | 0.1583886 | 0.5983568 | 0.158 | NA | NA |
| CYP19A1 | fluorouracil | 0.1588485 | 0.5857145 | 0.159 | NA | NA |
| DNMT3A | dasatinib | 0.1589015 | 0.8981810 | 0.159 | NA | NA |
| ALK | selumetinib | 0.1591782 | 0.4163122 | 0.15918 | NA | NA |
| KIT | erlotinib | 0.1599953 | 0.4945308 | 0.160 | NA | NA |
| CYP19A1 | belinostat | 0.1605668 | 0.9332615 | 0.16 | NA | NA |
| UGT1A1 | olaparib | 0.1608514 | 0.6836186 | 0.16085 | NA | NA |
| ABL1 | ruxolitinib | 0.1623760 | 0.9314078 | 0.1624 | NA | NA |
| PDGFRA | sunitinib | 0.1625269 | 0.5023558 | 0.16253 | NA | NA |
| AKT1 | vemurafenib | 0.1629510 | 0.3259020 | 0.16295 | NA | NA |
| CYP19A1 | nilotinib | 0.1633178 | 0.4627337 | 0.163 | NA | NA |
| RET | lapatinib | 0.1635140 | 0.6029902 | 0.1635 | NA | NA |
| ROS1 | ruxolitinib | 0.1652562 | 0.9314078 | 0.1653 | NA | NA |
| TPMT | gefitinib | 0.1653865 | 0.6634491 | 0.165 | NA | NA |
| CYP19A1 | cyclophosphamide | 0.1664216 | 0.8874508 | 0.166 | NA | NA |
| MET | cyclophosphamide | 0.1671638 | 0.8874508 | 0.167 | NA | NA |
| MGMT | temozolomide | 0.1678755 | 0.7065822 | 0.168 | NA | NA |
| ERBB2 | dasatinib | 0.1679727 | 0.8981810 | 0.168 | NA | NA |
| TSC1 | neratinib | 0.1690040 | 0.6384596 | 0.16900 | NA | NA |
| RET | vandetanib | 0.1691629 | 0.6681475 | 0.1692 | NA | NA |
| ROS1 | afatinib | 0.1715284 | 0.5539450 | 0.1715 | NA | NA |
| ALK | fluorouracil | 0.1722690 | 0.5857145 | 0.172 | NA | NA |
| IDH2 | fulvestrant | 0.1760724 | 0.7405746 | 0.1761 | NA | NA |
| BRCA2 | selumetinib | 0.1762300 | 0.4279871 | 0.17623 | NA | NA |
| IDH2 | imatinib | 0.1770530 | 0.6851658 | 0.1771 | NA | NA |
| TSC1 | dabrafenib | 0.1796741 | 0.8398900 | 0.17967 | NA | NA |
| ABL1 | belinostat | 0.1800207 | 0.9332615 | 0.18 | NA | NA |
| G6PD | gefitinib | 0.1809687 | 0.6634491 | 0.181 | NA | NA |
| PDGFRB | pazopanib | 0.1809713 | 0.6888301 | 0.1810 | NA | NA |
| ALK | lapatinib | 0.1820481 | 0.6029902 | 0.1820 | NA | NA |
| KIT | pazopanib | 0.1823374 | 0.6888301 | 0.1823 | NA | NA |
| UGT1A1 | cyclophosphamide | 0.1827105 | 0.8874508 | 0.183 | NA | NA |
| ESR1 | trametinib | 0.1839575 | 0.5233822 | 0.1840 | NA | NA |
| CYP19A1 | sunitinib | 0.1840148 | 0.5213753 | 0.18401 | NA | NA |
| RET | ruxolitinib | 0.1851983 | 0.9314078 | 0.1852 | NA | NA |
| MET | fulvestrant | 0.1858576 | 0.7405746 | 0.1859 | NA | NA |
| ALK | temozolomide | 0.1882566 | 0.7065822 | 0.188 | NA | NA |
| PDGFRA | trametinib | 0.1903208 | 0.5233822 | 0.1903 | NA | NA |
| MGMT | vandetanib | 0.1909706 | 0.6681475 | 0.1910 | NA | NA |
| JAK2 | azd | 0.1912155 | 0.5910299 | 0.191 | NA | NA |
| ERBB2 | afatinib | 0.1962848 | 0.5539450 | 0.1963 | NA | NA |
| DPYD | vemurafenib | 0.1972116 | 0.3725107 | 0.19721 | NA | NA |
| BRCA1 | cabozantinib | 0.1984399 | 0.4341695 | 0.1984 | NA | NA |
| IDH2 | afatinib | 0.2002219 | 0.5539450 | 0.2002 | NA | NA |
| BRCA1 | sunitinib | 0.2029629 | 0.5308261 | 0.20296 | NA | NA |
| PTCH1 | cabozantinib | 0.2043150 | 0.4341695 | 0.2043 | NA | NA |
| KRAS | temozolomide | 0.2044885 | 0.7065822 | 0.204 | NA | NA |
| RET | gefitinib | 0.2049189 | 0.6634491 | 0.205 | NA | NA |
| JAK2 | vandetanib | 0.2056568 | 0.6681475 | 0.2057 | NA | NA |
| TPMT | lapatinib | 0.2063631 | 0.6029902 | 0.2064 | NA | NA |
| ERBB2 | neratinib | 0.2066706 | 0.7012154 | 0.20667 | NA | NA |
| ABL1 | temozolomide | 0.2078183 | 0.7065822 | 0.208 | NA | NA |
| G6PD | vandetanib | 0.2082743 | 0.6681475 | 0.2083 | NA | NA |
| PDGFB | ruxolitinib | 0.2112854 | 0.9314078 | 0.2113 | NA | NA |
| JAK2 | regorafenib | 0.2116803 | 0.7996810 | 0.2117 | NA | NA |
| MGMT | afatinib | 0.2118025 | 0.5539450 | 0.2118 | NA | NA |
| TSC1 | ibrutinib | 0.2141178 | 0.7299037 | 0.2141 | NA | NA |
| RET | erlotinib | 0.2156089 | 0.5141116 | 0.216 | NA | NA |
| MET | trametinib | 0.2171377 | 0.5469503 | 0.2171 | NA | NA |
| TPMT | olaparib | 0.2193329 | 0.6914387 | 0.21933 | NA | NA |
| MET | vandetanib | 0.2195544 | 0.6681475 | 0.2196 | NA | NA |
| EGFR | azd | 0.2197291 | 0.5979347 | 0.220 | NA | NA |
| UGT1A1 | crizotinib | 0.2205241 | 0.6987047 | 0.221 | NA | NA |
| PDGFRA | cabozantinib | 0.2210144 | 0.4420288 | 0.2210 | NA | NA |
| AKT1 | erlotinib | 0.2216745 | 0.5141116 | 0.222 | NA | NA |
| ROS1 | lapatinib | 0.2232310 | 0.6029902 | 0.2232 | NA | NA |
| AKT1 | vandetanib | 0.2252466 | 0.6681475 | 0.2252 | NA | NA |
| DPYD | erlotinib | 0.2260758 | 0.5141116 | 0.226 | NA | NA |
| IDH2 | erlotinib | 0.2268140 | 0.5141116 | 0.227 | NA | NA |
| KIT | neratinib | 0.2272109 | 0.7012154 | 0.22721 | NA | NA |
| TSC1 | azd | 0.2297525 | 0.5979347 | 0.230 | NA | NA |
| NPM1 | fulvestrant | 0.2309231 | 0.7405746 | 0.2309 | NA | NA |
| MGMT | dasatinib | 0.2320758 | 0.8981810 | 0.232 | NA | NA |
| FLT3 | ibrutinib | 0.2324658 | 0.7299037 | 0.2325 | NA | NA |
| ROS1 | fulvestrant | 0.2343543 | 0.7405746 | 0.2344 | NA | NA |
| TPMT | vandetanib | 0.2358167 | 0.6681475 | 0.2358 | NA | NA |
| DPYD | gefitinib | 0.2382705 | 0.6634491 | 0.238 | NA | NA |
| RET | crizotinib | 0.2389903 | 0.6987047 | 0.239 | NA | NA |
| MGMT | lapatinib | 0.2397677 | 0.6029902 | 0.2398 | NA | NA |
| ROS1 | trametinib | 0.2403793 | 0.5469503 | 0.2404 | NA | NA |
| MYD88 | dabrafenib | 0.2408578 | 0.8398900 | 0.24086 | NA | NA |
| AKT1 | lapatinib | 0.2447114 | 0.6029902 | 0.2447 | NA | NA |
| PML | nilotinib | 0.2462058 | 0.6439228 | 0.246 | NA | NA |
| KIT | crizotinib | 0.2466017 | 0.6987047 | 0.247 | NA | NA |
| PDGFB | pazopanib | 0.2466642 | 0.7489184 | 0.2467 | NA | NA |
| RET | neratinib | 0.2474878 | 0.7012154 | 0.24749 | NA | NA |
| PDGFB | azd | 0.2475165 | 0.5979347 | 0.248 | NA | NA |
| MGMT | vemurafenib | 0.2488404 | 0.4452933 | 0.24884 | NA | NA |
| MGMT | gefitinib | 0.2498351 | 0.6634491 | 0.250 | NA | NA |
| MET | olaparib | 0.2511607 | 0.6914387 | 0.25116 | NA | NA |
| G6PD | sunitinib | 0.2518013 | 0.5738528 | 0.25180 | NA | NA |
| EGFR | afatinib | 0.2518397 | 0.6116107 | 0.2518 | NA | NA |
| TPMT | trametinib | 0.2520717 | 0.5469503 | 0.2521 | NA | NA |
| JAK2 | cyclophosphamide | 0.2532387 | 0.9645613 | 0.253 | NA | NA |
| TSC2 | cyclophosphamide | 0.2553250 | 0.9645613 | 0.255 | NA | NA |
| UGT1A1 | regorafenib | 0.2573217 | 0.8332306 | 0.2573 | NA | NA |
| MGMT | ruxolitinib | 0.2579077 | 0.9314078 | 0.2579 | NA | NA |
| NPM1 | ibrutinib | 0.2580132 | 0.7299037 | 0.2580 | NA | NA |
| PDGFRB | ibrutinib | 0.2584041 | 0.7299037 | 0.2584 | NA | NA |
| TPMT | pazopanib | 0.2589317 | 0.7489184 | 0.2589 | NA | NA |
| AKT1 | olaparib | 0.2619009 | 0.6914387 | 0.26190 | NA | NA |
| IDH2 | lapatinib | 0.2631941 | 0.6029902 | 0.2632 | NA | NA |
| PML | olaparib | 0.2632816 | 0.6914387 | 0.26328 | NA | NA |
| MET | pazopanib | 0.2643242 | 0.7489184 | 0.2643 | NA | NA |
| TSC2 | azd | 0.2666255 | 0.5979347 | 0.267 | NA | NA |
| TSC1 | dasatinib | 0.2684477 | 0.8981810 | 0.268 | NA | NA |
| MYD88 | cabozantinib | 0.2705198 | 0.5109818 | 0.2705 | NA | NA |
| AKT1 | gefitinib | 0.2710276 | 0.6634491 | 0.271 | NA | NA |
| MYD88 | lapatinib | 0.2727428 | 0.6029902 | 0.2727 | NA | NA |
| JAK2 | fulvestrant | 0.2731170 | 0.7405746 | 0.2731 | NA | NA |
| CYP19A1 | lapatinib | 0.2738891 | 0.6029902 | 0.2739 | NA | NA |
| ERBB2 | gefitinib | 0.2741193 | 0.6634491 | 0.274 | NA | NA |
| PDGFRA | selumetinib | 0.2749493 | 0.6232184 | 0.27495 | NA | NA |
| KRAS | fulvestrant | 0.2766131 | 0.7405746 | 0.2766 | NA | NA |
| TSC1 | imatinib | 0.2772743 | 0.6851658 | 0.2773 | NA | NA |
| MGMT | trametinib | 0.2783193 | 0.5469503 | 0.2783 | NA | NA |
| ALK | imatinib | 0.2787671 | 0.6851658 | 0.2788 | NA | NA |
| MGMT | fulvestrant | 0.2788073 | 0.7405746 | 0.2788 | NA | NA |
| AKT1 | ibrutinib | 0.2790808 | 0.7299037 | 0.2791 | NA | NA |
| ROS1 | sunitinib | 0.2791187 | 0.5738528 | 0.27912 | NA | NA |
| FLT3 | dabrafenib | 0.2794287 | 0.8398900 | 0.27943 | NA | NA |
| ABL1 | fulvestrant | 0.2803031 | 0.7405746 | 0.2803 | NA | NA |
| TSC2 | sunitinib | 0.2822305 | 0.5738528 | 0.28223 | NA | NA |
| ERBB2 | trametinib | 0.2825628 | 0.5469503 | 0.2826 | NA | NA |
| CYP19A1 | fulvestrant | 0.2831609 | 0.7405746 | 0.2832 | NA | NA |
| BRCA1 | lapatinib | 0.2837601 | 0.6029902 | 0.2838 | NA | NA |
| EGFR | vandetanib | 0.2853916 | 0.6968774 | 0.2854 | NA | NA |
| PTCH1 | dasatinib | 0.2856356 | 0.8981810 | 0.286 | NA | NA |
| ERBB3 | sunitinib | 0.2869264 | 0.5738528 | 0.28693 | NA | NA |
| ESR1 | olaparib | 0.2881802 | 0.6914387 | 0.28818 | NA | NA |
| TPMT | fluorouracil | 0.2892300 | 0.8392181 | 0.289 | NA | NA |
| MET | regorafenib | 0.2896133 | 0.8332306 | 0.2896 | NA | NA |
| PDGFRB | neratinib | 0.2911880 | 0.7411173 | 0.29119 | NA | NA |
| IDH2 | vandetanib | 0.2935755 | 0.6968774 | 0.2936 | NA | NA |
| ERBB2 | imatinib | 0.2961755 | 0.6851658 | 0.2962 | NA | NA |
| NPM1 | azd | 0.2976666 | 0.5979347 | 0.298 | NA | NA |
| DPYD | belinostat | 0.2978744 | 0.9332615 | 0.30 | NA | NA |
| UGT1A1 | ruxolitinib | 0.2979995 | 0.9314078 | 0.2980 | NA | NA |
| TSC2 | dasatinib | 0.2997123 | 0.8981810 | 0.300 | NA | NA |
| MGMT | nilotinib | 0.3000538 | 0.6835150 | 0.300 | NA | NA |
| NPM1 | cabozantinib | 0.3013980 | 0.5150108 | 0.3014 | NA | NA |
| ABL1 | crizotinib | 0.3022158 | 0.7904106 | 0.302 | NA | NA |
| PTCH1 | azd | 0.3023110 | 0.5979347 | 0.302 | NA | NA |
| ABL1 | cabozantinib | 0.3029475 | 0.5150108 | 0.3029 | NA | NA |
| CYP19A1 | olaparib | 0.3043830 | 0.6914387 | 0.30438 | NA | NA |
| ESR1 | gefitinib | 0.3045810 | 0.6634491 | 0.305 | NA | NA |
| PDGFB | neratinib | 0.3051659 | 0.7411173 | 0.30517 | NA | NA |
| ALK | vemurafenib | 0.3064787 | 0.5210137 | 0.30648 | NA | NA |
| PDGFRA | vandetanib | 0.3074459 | 0.6968774 | 0.3074 | NA | NA |
| AKT1 | afatinib | 0.3079994 | 0.6638151 | 0.3080 | NA | NA |
| BRAF | belinostat | 0.3085030 | 0.9332615 | 0.31 | NA | NA |
| TSC1 | selumetinib | 0.3094377 | 0.6575550 | 0.30944 | NA | NA |
| DNMT3A | imatinib | 0.3100619 | 0.6851658 | 0.3101 | NA | NA |
| TPMT | erlotinib | 0.3109754 | 0.6608228 | 0.311 | NA | NA |
| PML | trametinib | 0.3122459 | 0.5469503 | 0.3122 | NA | NA |
| ALK | trametinib | 0.3149108 | 0.5469503 | 0.3149 | NA | NA |
| RET | dasatinib | 0.3153187 | 0.8981810 | 0.315 | NA | NA |
| UGT1A1 | imatinib | 0.3163786 | 0.6851658 | 0.3164 | NA | NA |
| MYD88 | gefitinib | 0.3170349 | 0.6634491 | 0.317 | NA | NA |
| EGFR | olaparib | 0.3170528 | 0.6914387 | 0.31705 | NA | NA |
| MYD88 | ibrutinib | 0.3177454 | 0.7476014 | 0.3177 | NA | NA |
| FLT3 | pazopanib | 0.3190784 | 0.8345127 | 0.3191 | NA | NA |
| ROS1 | temozolomide | 0.3206533 | 0.7644487 | 0.321 | NA | NA |
| TSC2 | nilotinib | 0.3227612 | 0.6835150 | 0.323 | NA | NA |
| BRCA1 | temozolomide | 0.3234468 | 0.7644487 | 0.323 | NA | NA |
| PDGFRA | regorafenib | 0.3247031 | 0.8332306 | 0.3247 | NA | NA |
| G6PD | cabozantinib | 0.3251186 | 0.5263825 | 0.3251 | NA | NA |
| ALK | olaparib | 0.3253829 | 0.6914387 | 0.32538 | NA | NA |
| IDH2 | dabrafenib | 0.3256308 | 0.8398900 | 0.32563 | NA | NA |
| PDGFRB | ruxolitinib | 0.3271325 | 0.9314078 | 0.3271 | NA | NA |
| PDGFB | imatinib | 0.3290742 | 0.6851658 | 0.3291 | NA | NA |
| BRCA1 | regorafenib | 0.3293828 | 0.8332306 | 0.3294 | NA | NA |
| ABL1 | fluorouracil | 0.3296373 | 0.8392181 | 0.330 | NA | NA |
| UGT1A1 | ibrutinib | 0.3298241 | 0.7476014 | 0.3298 | NA | NA |
| ERBB3 | imatinib | 0.3301067 | 0.6851658 | 0.3301 | NA | NA |
| ESR1 | lapatinib | 0.3306838 | 0.6259186 | 0.3307 | NA | NA |
| TPMT | azd | 0.3307900 | 0.5979347 | 0.331 | NA | NA |
| MET | lapatinib | 0.3313687 | 0.6259186 | 0.3314 | NA | NA |
| KIT | gefitinib | 0.3317245 | 0.6634491 | 0.332 | NA | NA |
| MYD88 | afatinib | 0.3320613 | 0.6638151 | 0.3321 | NA | NA |
| PDGFRA | fluorouracil | 0.3334048 | 0.8392181 | 0.333 | NA | NA |
| IDH2 | neratinib | 0.3337619 | 0.7446930 | 0.33376 | NA | NA |
| MYD88 | azd | 0.3389331 | 0.5979347 | 0.339 | NA | NA |
| PML | imatinib | 0.3392370 | 0.6851658 | 0.3392 | NA | NA |
| ERBB2 | selumetinib | 0.3397053 | 0.6794106 | 0.33971 | NA | NA |
| ABL1 | afatinib | 0.3423060 | 0.6638151 | 0.3423 | NA | NA |
| KRAS | imatinib | 0.3425829 | 0.6851658 | 0.3426 | NA | NA |
| TSC1 | regorafenib | 0.3430949 | 0.8332306 | 0.3431 | NA | NA |
| ESR1 | nilotinib | 0.3452748 | 0.6835150 | 0.345 | NA | NA |
| NPM1 | fluorouracil | 0.3455604 | 0.8392181 | 0.346 | NA | NA |
| BRAF | nilotinib | 0.3473234 | 0.6835150 | 0.347 | NA | NA |
| ERBB3 | belinostat | 0.3479934 | 0.9332615 | 0.35 | NA | NA |
| IDH2 | cabozantinib | 0.3499020 | 0.5407576 | 0.3499 | NA | NA |
| NPM1 | neratinib | 0.3504438 | 0.7446930 | 0.35044 | NA | NA |
| TSC2 | afatinib | 0.3514315 | 0.6638151 | 0.3514 | NA | NA |
| KRAS | dasatinib | 0.3522956 | 0.8981810 | 0.352 | NA | NA |
| ERBB3 | cyclophosphamide | 0.3561490 | 0.9793614 | 0.356 | NA | NA |
| IDH2 | azd | 0.3568667 | 0.5979347 | 0.357 | NA | NA |
| PDGFB | dasatinib | 0.3571989 | 0.8981810 | 0.357 | NA | NA |
| NPM1 | dabrafenib | 0.3577714 | 0.8398900 | 0.35777 | NA | NA |
| BRAF | fulvestrant | 0.3578334 | 0.8690240 | 0.3578 | NA | NA |
| ALK | gefitinib | 0.3595266 | 0.6791058 | 0.360 | NA | NA |
| NPM1 | temozolomide | 0.3616494 | 0.7644487 | 0.362 | NA | NA |
| PDGFB | nilotinib | 0.3618609 | 0.6835150 | 0.362 | NA | NA |
| UGT1A1 | temozolomide | 0.3627228 | 0.7644487 | 0.363 | NA | NA |
| MET | dabrafenib | 0.3629609 | 0.8398900 | 0.36296 | NA | NA |
| PDGFRB | belinostat | 0.3636843 | 0.9332615 | 0.36 | NA | NA |
| ERBB3 | lapatinib | 0.3667711 | 0.6475307 | 0.3668 | NA | NA |
| IDH2 | vemurafenib | 0.3678300 | 0.5955342 | 0.36783 | NA | NA |
| TPMT | regorafenib | 0.3679816 | 0.8340916 | 0.3680 | NA | NA |
| ERBB3 | azd | 0.3693126 | 0.5979347 | 0.369 | NA | NA |
| JAK2 | afatinib | 0.3737944 | 0.6674950 | 0.3738 | NA | NA |
| FLT3 | temozolomide | 0.3743174 | 0.7644487 | 0.374 | NA | NA |
| ROS1 | cyclophosphamide | 0.3774686 | 0.9793614 | 0.377 | NA | NA |
| ABL1 | ibrutinib | 0.3777841 | 0.8027912 | 0.3778 | NA | NA |
| PDGFRA | pazopanib | 0.3783240 | 0.9187869 | 0.3783 | NA | NA |
| EGFR | lapatinib | 0.3809004 | 0.6475307 | 0.3809 | NA | NA |
| PML | sunitinib | 0.3810854 | 0.7198280 | 0.38109 | NA | NA |
| BRCA2 | trametinib | 0.3821071 | 0.6252529 | 0.3821 | NA | NA |
| EGFR | ruxolitinib | 0.3825743 | 0.9314078 | 0.3826 | NA | NA |
| PML | dasatinib | 0.3857611 | 0.8981810 | 0.386 | NA | NA |
| MGMT | neratinib | 0.3926360 | 0.7852720 | 0.39264 | NA | NA |
| PML | afatinib | 0.3926441 | 0.6674950 | 0.3926 | NA | NA |
| BRAF | cabozantinib | 0.3934771 | 0.5686724 | 0.3935 | NA | NA |
| ROS1 | vemurafenib | 0.3937304 | 0.6084924 | 0.39373 | NA | NA |
| ERBB3 | dabrafenib | 0.3967421 | 0.8398900 | 0.39674 | NA | NA |
| TPMT | cyclophosphamide | 0.3978413 | 0.9793614 | 0.398 | NA | NA |
| RET | belinostat | 0.3979105 | 0.9332615 | 0.40 | NA | NA |
| ALK | dabrafenib | 0.3998459 | 0.8398900 | 0.39985 | NA | NA |
| PDGFRA | dasatinib | 0.4012694 | 0.8981810 | 0.401 | NA | NA |
| NPM1 | vandetanib | 0.4033915 | 0.8222586 | 0.4034 | NA | NA |
| PML | ruxolitinib | 0.4077983 | 0.9314078 | 0.4078 | NA | NA |
| AKT1 | trametinib | 0.4079935 | 0.6252529 | 0.4080 | NA | NA |
| KIT | dabrafenib | 0.4097454 | 0.8398900 | 0.40975 | NA | NA |
| RET | regorafenib | 0.4107421 | 0.8471493 | 0.4107 | NA | NA |
| ERBB3 | vandetanib | 0.4111293 | 0.8222586 | 0.4111 | NA | NA |
| KRAS | dabrafenib | 0.4111914 | 0.8398900 | 0.41119 | NA | NA |
| DPYD | temozolomide | 0.4129554 | 0.7644487 | 0.413 | NA | NA |
| FLT3 | lapatinib | 0.4146955 | 0.6714118 | 0.4147 | NA | NA |
| ESR1 | temozolomide | 0.4151428 | 0.7644487 | 0.415 | NA | NA |
| BRCA2 | cabozantinib | 0.4162945 | 0.5686724 | 0.4163 | NA | NA |
| TSC2 | trametinib | 0.4168352 | 0.6252529 | 0.4168 | NA | NA |
| PML | erlotinib | 0.4170584 | 0.8218115 | 0.417 | NA | NA |
| CYP19A1 | cabozantinib | 0.4181415 | 0.5686724 | 0.4181 | NA | NA |
| JAK2 | crizotinib | 0.4182454 | 0.9896386 | 0.418 | NA | NA |
| ALK | fulvestrant | 0.4191815 | 0.9110805 | 0.4192 | NA | NA |
| PTCH1 | selumetinib | 0.4194027 | 0.7472482 | 0.41940 | NA | NA |
| EGFR | dasatinib | 0.4226734 | 0.8981810 | 0.423 | NA | NA |
| BRCA2 | azd | 0.4237037 | 0.6548149 | 0.424 | NA | NA |
| KIT | cyclophosphamide | 0.4256579 | 0.9793614 | 0.426 | NA | NA |
| ESR1 | ibrutinib | 0.4291778 | 0.8107592 | 0.4292 | NA | NA |
| EGFR | ibrutinib | 0.4292255 | 0.8107592 | 0.4292 | NA | NA |
| NPM1 | selumetinib | 0.4302455 | 0.7472482 | 0.43025 | NA | NA |
| PML | pazopanib | 0.4313542 | 0.9261994 | 0.4314 | NA | NA |
| TPMT | dabrafenib | 0.4326706 | 0.8398900 | 0.43267 | NA | NA |
| PDGFRB | fluorouracil | 0.4341969 | 0.8677771 | 0.434 | NA | NA |
| PML | temozolomide | 0.4354604 | 0.7644487 | 0.435 | NA | NA |
| ESR1 | cabozantinib | 0.4356954 | 0.5697555 | 0.4357 | NA | NA |
| ERBB3 | ruxolitinib | 0.4364470 | 0.9314078 | 0.4364 | NA | NA |
| MYD88 | fulvestrant | 0.4383092 | 0.9110805 | 0.4383 | NA | NA |
| CYP19A1 | temozolomide | 0.4385706 | 0.7644487 | 0.439 | NA | NA |
| IDH2 | trametinib | 0.4390903 | 0.6262131 | 0.4391 | NA | NA |
| ESR1 | sunitinib | 0.4399411 | 0.7545287 | 0.43994 | NA | NA |
| BRCA2 | vandetanib | 0.4404474 | 0.8272351 | 0.4404 | NA | NA |
| IDH2 | selumetinib | 0.4434340 | 0.7472482 | 0.44343 | NA | NA |
| ALK | nilotinib | 0.4451309 | 0.7927775 | 0.445 | NA | NA |
| TSC2 | neratinib | 0.4493579 | 0.8334472 | 0.44936 | NA | NA |
| MET | temozolomide | 0.4496757 | 0.7644487 | 0.450 | NA | NA |
| ERBB3 | pazopanib | 0.4547800 | 0.9261994 | 0.4548 | NA | NA |
| IDH2 | dasatinib | 0.4572773 | 0.9092193 | 0.457 | NA | NA |
| ESR1 | erlotinib | 0.4580536 | 0.8218115 | 0.458 | NA | NA |
| BRAF | erlotinib | 0.4592476 | 0.8218115 | 0.459 | NA | NA |
| G6PD | vemurafenib | 0.4602214 | 0.6539778 | 0.46022 | NA | NA |
| ESR1 | vemurafenib | 0.4616314 | 0.6539778 | 0.46163 | NA | NA |
| BRAF | vandetanib | 0.4622785 | 0.8272351 | 0.4623 | NA | NA |
| PDGFB | fluorouracil | 0.4641195 | 0.8677771 | 0.464 | NA | NA |
| MGMT | sunitinib | 0.4645056 | 0.7545287 | 0.46451 | NA | NA |
| JAK2 | sunitinib | 0.4660324 | 0.7545287 | 0.46603 | NA | NA |
| FLT3 | regorafenib | 0.4660591 | 0.8471493 | 0.4661 | NA | NA |
| G6PD | fluorouracil | 0.4661924 | 0.8677771 | 0.466 | NA | NA |
| ABL1 | gefitinib | 0.4664039 | 0.8346175 | 0.466 | NA | NA |
| AKT1 | ruxolitinib | 0.4679864 | 0.9314078 | 0.4680 | NA | NA |
| TPMT | ibrutinib | 0.4703605 | 0.8416977 | 0.4704 | NA | NA |
| DNMT3A | cabozantinib | 0.4741169 | 0.5970360 | 0.4741 | NA | NA |
| ERBB2 | azd | 0.4751190 | 0.6739725 | 0.475 | NA | NA |
| CYP19A1 | azd | 0.4757453 | 0.6739725 | 0.476 | NA | NA |
| KIT | regorafenib | 0.4759780 | 0.8471493 | 0.4760 | NA | NA |
| CYP19A1 | selumetinib | 0.4763756 | 0.7472482 | 0.47638 | NA | NA |
| UGT1A1 | fluorouracil | 0.4767219 | 0.8677771 | 0.477 | NA | NA |
| BRCA2 | afatinib | 0.4780707 | 0.7569737 | 0.4781 | NA | NA |
| MYD88 | trametinib | 0.4783281 | 0.6262131 | 0.4783 | NA | NA |
| BRCA2 | crizotinib | 0.4789637 | 0.9896386 | 0.479 | NA | NA |
| BRCA1 | neratinib | 0.4793342 | 0.8334472 | 0.47933 | NA | NA |
| BRCA1 | imatinib | 0.4803511 | 0.9073299 | 0.4804 | NA | NA |
| G6PD | dasatinib | 0.4813514 | 0.9092193 | 0.481 | NA | NA |
| EGFR | dabrafenib | 0.4817681 | 0.8681874 | 0.48177 | NA | NA |
| JAK2 | trametinib | 0.4825043 | 0.6262131 | 0.4825 | NA | NA |
| G6PD | lapatinib | 0.4825811 | 0.7270249 | 0.4826 | NA | NA |
| IDH2 | pazopanib | 0.4829493 | 0.9261994 | 0.4829 | NA | NA |
| ABL1 | selumetinib | 0.4835135 | 0.7472482 | 0.48351 | NA | NA |
| MGMT | belinostat | 0.4836415 | 0.9332615 | 0.48 | NA | NA |
| BRCA2 | belinostat | 0.4837494 | 0.9332615 | 0.48 | NA | NA |
| FLT3 | belinostat | 0.4844586 | 0.9332615 | 0.48 | NA | NA |
| BRCA1 | fluorouracil | 0.4849343 | 0.8677771 | 0.485 | NA | NA |
| DNMT3A | temozolomide | 0.4872219 | 0.7776868 | 0.487 | NA | NA |
| ALK | regorafenib | 0.4873433 | 0.8471493 | 0.4873 | NA | NA |
| DPYD | ruxolitinib | 0.4879108 | 0.9314078 | 0.4879 | NA | NA |
| MET | afatinib | 0.4898065 | 0.7569737 | 0.4898 | NA | NA |
| PDGFRA | neratinib | 0.4902631 | 0.8334472 | 0.49026 | NA | NA |
| MGMT | crizotinib | 0.4938707 | 0.9896386 | 0.494 | NA | NA |
| TSC1 | vandetanib | 0.4950385 | 0.8415654 | 0.4950 | NA | NA |
| DPYD | lapatinib | 0.4952434 | 0.7270249 | 0.4952 | NA | NA |
| PTCH1 | pazopanib | 0.4968297 | 0.9261994 | 0.4968 | NA | NA |
| TSC1 | temozolomide | 0.5032091 | 0.7776868 | 0.503 | NA | NA |
| DPYD | cyclophosphamide | 0.5045811 | 0.9793614 | 0.505 | NA | NA |
| RET | sunitinib | 0.5118218 | 0.7868747 | 0.51182 | NA | NA |
| DPYD | trametinib | 0.5123073 | 0.6262131 | 0.5123 | NA | NA |
| UGT1A1 | trametinib | 0.5123562 | 0.6262131 | 0.5124 | NA | NA |
| PML | lapatinib | 0.5131940 | 0.7270249 | 0.5132 | NA | NA |
| MET | neratinib | 0.5169277 | 0.8369306 | 0.51693 | NA | NA |
| RET | pazopanib | 0.5175936 | 0.9261994 | 0.5176 | NA | NA |
| TSC2 | ruxolitinib | 0.5176922 | 0.9314078 | 0.5177 | NA | NA |
| DPYD | dabrafenib | 0.5177549 | 0.8681874 | 0.51775 | NA | NA |
| BRCA1 | gefitinib | 0.5187110 | 0.8466777 | 0.519 | NA | NA |
| PDGFRA | nilotinib | 0.5194411 | 0.7927775 | 0.519 | NA | NA |
| ABL1 | regorafenib | 0.5196255 | 0.8471493 | 0.5196 | NA | NA |
| NPM1 | gefitinib | 0.5229480 | 0.8466777 | 0.523 | NA | NA |
| DPYD | regorafenib | 0.5244529 | 0.8471493 | 0.5245 | NA | NA |
| BRCA2 | olaparib | 0.5281161 | 0.9728161 | 0.52812 | NA | NA |
| DNMT3A | nilotinib | 0.5289852 | 0.7927775 | 0.529 | NA | NA |
| AKT1 | cyclophosphamide | 0.5303222 | 0.9793614 | 0.530 | NA | NA |
| PDGFRA | ruxolitinib | 0.5303811 | 0.9314078 | 0.5304 | NA | NA |
| KIT | sunitinib | 0.5322976 | 0.7868747 | 0.53230 | NA | NA |
| FLT3 | dasatinib | 0.5331194 | 0.9367075 | 0.533 | NA | NA |
| G6PD | cyclophosphamide | 0.5360224 | 0.9793614 | 0.536 | NA | NA |
| ERBB3 | crizotinib | 0.5361343 | 0.9896386 | 0.536 | NA | NA |
| MYD88 | imatinib | 0.5393201 | 0.9425360 | 0.5393 | NA | NA |
| TSC1 | lapatinib | 0.5398720 | 0.7342259 | 0.5399 | NA | NA |
| RET | vemurafenib | 0.5409337 | 0.7294806 | 0.54093 | NA | NA |
| BRCA2 | dabrafenib | 0.5419188 | 0.8681874 | 0.54192 | NA | NA |
| TSC2 | crizotinib | 0.5427013 | 0.9896386 | 0.543 | NA | NA |
| PTCH1 | fulvestrant | 0.5427377 | 0.9110805 | 0.5427 | NA | NA |
| BRCA2 | cyclophosphamide | 0.5442614 | 0.9793614 | 0.544 | NA | NA |
| NPM1 | nilotinib | 0.5448245 | 0.7927775 | 0.545 | NA | NA |
| EGFR | erlotinib | 0.5472418 | 0.8891239 | 0.547 | NA | NA |
| EGFR | nilotinib | 0.5479716 | 0.7927775 | 0.548 | NA | NA |
| ESR1 | regorafenib | 0.5481555 | 0.8471493 | 0.5482 | NA | NA |
| TSC2 | erlotinib | 0.5491647 | 0.8891239 | 0.549 | NA | NA |
| ERBB3 | selumetinib | 0.5514235 | 0.8151478 | 0.55142 | NA | NA |
| MGMT | azd | 0.5517454 | 0.7386733 | 0.552 | NA | NA |
| TSC2 | temozolomide | 0.5520727 | 0.8087434 | 0.552 | NA | NA |
| MYD88 | neratinib | 0.5522299 | 0.8534462 | 0.55223 | NA | NA |
| JAK2 | dabrafenib | 0.5524829 | 0.8681874 | 0.55248 | NA | NA |
| IDH2 | ruxolitinib | 0.5558028 | 0.9314078 | 0.5558 | NA | NA |
| PDGFRB | fulvestrant | 0.5559160 | 0.9110805 | 0.5559 | NA | NA |
| PDGFB | gefitinib | 0.5559298 | 0.8546038 | 0.556 | NA | NA |
| ERBB2 | vemurafenib | 0.5578381 | 0.7294806 | 0.55784 | NA | NA |
| TSC2 | vandetanib | 0.5599331 | 0.8665251 | 0.5599 | NA | NA |
| ERBB2 | vandetanib | 0.5606927 | 0.8665251 | 0.5607 | NA | NA |
| PDGFRB | nilotinib | 0.5622570 | 0.7927775 | 0.562 | NA | NA |
| JAK2 | ibrutinib | 0.5688103 | 0.9669776 | 0.5688 | NA | NA |
| RET | fulvestrant | 0.5689282 | 0.9110805 | 0.5689 | NA | NA |
| MGMT | olaparib | 0.5699313 | 0.9728161 | 0.56993 | NA | NA |
| PDGFB | olaparib | 0.5706892 | 0.9728161 | 0.57069 | NA | NA |
| FLT3 | fulvestrant | 0.5722357 | 0.9110805 | 0.5722 | NA | NA |
| KRAS | cyclophosphamide | 0.5770737 | 0.9793614 | 0.577 | NA | NA |
| PML | belinostat | 0.5778444 | 0.9332615 | 0.58 | NA | NA |
| PDGFRB | gefitinib | 0.5781143 | 0.8546038 | 0.578 | NA | NA |
| DPYD | sunitinib | 0.5784482 | 0.8194683 | 0.57845 | NA | NA |
| MYD88 | pazopanib | 0.5788620 | 0.9261994 | 0.5789 | NA | NA |
| UGT1A1 | afatinib | 0.5812670 | 0.8592643 | 0.5813 | NA | NA |
| ABL1 | imatinib | 0.5818558 | 0.9425360 | 0.5819 | NA | NA |
| FLT3 | imatinib | 0.5821546 | 0.9425360 | 0.5822 | NA | NA |
| ERBB3 | nilotinib | 0.5829246 | 0.7927775 | 0.583 | NA | NA |
| DNMT3A | cyclophosphamide | 0.5843537 | 0.9793614 | 0.584 | NA | NA |
| PML | cabozantinib | 0.5847529 | 0.6901833 | 0.5848 | NA | NA |
| ROS1 | belinostat | 0.5877641 | 0.9332615 | 0.59 | NA | NA |
| AKT1 | temozolomide | 0.5884213 | 0.8087434 | 0.588 | NA | NA |
| KIT | lapatinib | 0.5885275 | 0.7696129 | 0.5885 | NA | NA |
| ERBB3 | fulvestrant | 0.5897197 | 0.9110805 | 0.5897 | NA | NA |
| KIT | azd | 0.5928965 | 0.7386733 | 0.593 | NA | NA |
| PDGFRB | temozolomide | 0.5946643 | 0.8087434 | 0.595 | NA | NA |
| DPYD | cabozantinib | 0.5989674 | 0.6901833 | 0.5990 | NA | NA |
| G6PD | ibrutinib | 0.6023586 | 0.9736731 | 0.6024 | NA | NA |
| DNMT3A | vemurafenib | 0.6061305 | 0.7525336 | 0.60613 | NA | NA |
| MET | azd | 0.6072926 | 0.7386733 | 0.607 | NA | NA |
| G6PD | azd | 0.6083192 | 0.7386733 | 0.608 | NA | NA |
| MGMT | cyclophosphamide | 0.6089169 | 0.9793614 | 0.609 | NA | NA |
| RET | cabozantinib | 0.6089852 | 0.6901833 | 0.6090 | NA | NA |
| PDGFB | erlotinib | 0.6129494 | 0.9151456 | 0.613 | NA | NA |
| MYD88 | ruxolitinib | 0.6181728 | 0.9314078 | 0.6182 | NA | NA |
| ABL1 | nilotinib | 0.6182260 | 0.8084494 | 0.618 | NA | NA |
| CYP19A1 | vandetanib | 0.6183456 | 0.8720434 | 0.6183 | NA | NA |
| TSC1 | trametinib | 0.6186725 | 0.7291497 | 0.6187 | NA | NA |
| ERBB2 | temozolomide | 0.6194974 | 0.8101120 | 0.619 | NA | NA |
| PDGFRB | vemurafenib | 0.6197336 | 0.7525336 | 0.61973 | NA | NA |
| TSC1 | olaparib | 0.6197994 | 0.9728161 | 0.61980 | NA | NA |
| BRCA1 | pazopanib | 0.6211989 | 0.9261994 | 0.6212 | NA | NA |
| PDGFRA | dabrafenib | 0.6212605 | 0.9318907 | 0.62126 | NA | NA |
| BRCA1 | dasatinib | 0.6214626 | 0.9367075 | 0.621 | NA | NA |
| NPM1 | ruxolitinib | 0.6223011 | 0.9314078 | 0.6223 | NA | NA |
| TSC2 | lapatinib | 0.6258155 | 0.7879401 | 0.6258 | NA | NA |
| CYP19A1 | ruxolitinib | 0.6276320 | 0.9314078 | 0.6276 | NA | NA |
| ERBB2 | ruxolitinib | 0.6293981 | 0.9314078 | 0.6294 | NA | NA |
| DNMT3A | ruxolitinib | 0.6300700 | 0.9314078 | 0.6301 | NA | NA |
| KIT | vandetanib | 0.6306055 | 0.8720434 | 0.6306 | NA | NA |
| AKT1 | regorafenib | 0.6309258 | 0.9326729 | 0.6309 | NA | NA |
| AKT1 | fluorouracil | 0.6312805 | 0.9561079 | 0.631 | NA | NA |
| RET | imatinib | 0.6313687 | 0.9504694 | 0.6314 | NA | NA |
| ESR1 | azd | 0.6359850 | 0.7424789 | 0.636 | NA | NA |
| IDH2 | crizotinib | 0.6363824 | 0.9896386 | 0.636 | NA | NA |
| TSC1 | erlotinib | 0.6364596 | 0.9151456 | 0.636 | NA | NA |
| ERBB3 | gefitinib | 0.6397928 | 0.8848141 | 0.640 | NA | NA |
| TSC1 | crizotinib | 0.6420105 | 0.9896386 | 0.642 | NA | NA |
| KIT | imatinib | 0.6429646 | 0.9504694 | 0.6430 | NA | NA |
| AKT1 | pazopanib | 0.6440994 | 0.9261994 | 0.6441 | NA | NA |
| PDGFB | selumetinib | 0.6445370 | 0.8818646 | 0.64454 | NA | NA |
| MET | erlotinib | 0.6459851 | 0.9151456 | 0.646 | NA | NA |
| BRCA1 | selumetinib | 0.6484298 | 0.8818646 | 0.64843 | NA | NA |
| PDGFRA | afatinib | 0.6518163 | 0.8631215 | 0.6518 | NA | NA |
| DNMT3A | azd | 0.6551284 | 0.7424789 | 0.655 | NA | NA |
| MYD88 | fluorouracil | 0.6552215 | 0.9561079 | 0.655 | NA | NA |
| IDH2 | cyclophosphamide | 0.6554963 | 0.9793614 | 0.655 | NA | NA |
| UGT1A1 | neratinib | 0.6590084 | 0.9509752 | 0.65901 | NA | NA |
| BRCA2 | ibrutinib | 0.6602730 | 0.9736731 | 0.6603 | NA | NA |
| PTCH1 | belinostat | 0.6603291 | 0.9332615 | 0.66 | NA | NA |
| UGT1A1 | lapatinib | 0.6619661 | 0.7879401 | 0.6620 | NA | NA |
| TSC1 | pazopanib | 0.6622597 | 0.9261994 | 0.6623 | NA | NA |
| BRAF | regorafenib | 0.6631522 | 0.9394657 | 0.6632 | NA | NA |
| AKT1 | dasatinib | 0.6650170 | 0.9367075 | 0.665 | NA | NA |
| ALK | belinostat | 0.6654501 | 0.9332615 | 0.67 | NA | NA |
| G6PD | afatinib | 0.6656317 | 0.8631215 | 0.6656 | NA | NA |
| PDGFRA | fulvestrant | 0.6659409 | 0.9110805 | 0.6659 | NA | NA |
| PML | dabrafenib | 0.6659420 | 0.9324432 | 0.66594 | NA | NA |
| RET | nilotinib | 0.6667141 | 0.8395660 | 0.667 | NA | NA |
| BRCA2 | lapatinib | 0.6720665 | 0.7879401 | 0.6721 | NA | NA |
| NPM1 | cyclophosphamide | 0.6729128 | 0.9793614 | 0.673 | NA | NA |
| G6PD | fulvestrant | 0.6741823 | 0.9110805 | 0.6742 | NA | NA |
| PDGFRB | crizotinib | 0.6743149 | 0.9896386 | 0.674 | NA | NA |
| ESR1 | fulvestrant | 0.6748204 | 0.9110805 | 0.6748 | NA | NA |
| KIT | olaparib | 0.6772410 | 0.9728161 | 0.67724 | NA | NA |
| ESR1 | neratinib | 0.6776713 | 0.9509752 | 0.67767 | NA | NA |
| PTCH1 | dabrafenib | 0.6781405 | 0.9324432 | 0.67814 | NA | NA |
| ABL1 | azd | 0.6783940 | 0.7440450 | 0.678 | NA | NA |
| ABL1 | olaparib | 0.6795493 | 0.9728161 | 0.67955 | NA | NA |
| EGFR | cabozantinib | 0.6800714 | 0.7458848 | 0.6801 | NA | NA |
| ALK | ruxolitinib | 0.6822022 | 0.9664531 | 0.6822 | NA | NA |
| UGT1A1 | gefitinib | 0.6824391 | 0.8848141 | 0.682 | NA | NA |
| ABL1 | vandetanib | 0.6832739 | 0.8720434 | 0.6833 | NA | NA |
| TSC1 | fulvestrant | 0.6874271 | 0.9110805 | 0.6874 | NA | NA |
| PTCH1 | fluorouracil | 0.6889362 | 0.9561079 | 0.689 | NA | NA |
| PTCH1 | crizotinib | 0.6896847 | 0.9896386 | 0.690 | NA | NA |
| ERBB2 | belinostat | 0.6914232 | 0.9332615 | 0.69 | NA | NA |
| CYP19A1 | afatinib | 0.6916918 | 0.8631215 | 0.6917 | NA | NA |
| JAK2 | olaparib | 0.6925765 | 0.9728161 | 0.69258 | NA | NA |
| PML | regorafenib | 0.6943881 | 0.9410069 | 0.6944 | NA | NA |
| ERBB3 | afatinib | 0.6959010 | 0.8631215 | 0.6959 | NA | NA |
| EGFR | fulvestrant | 0.6967086 | 0.9110805 | 0.6967 | NA | NA |
| BRCA2 | dasatinib | 0.6990595 | 0.9367075 | 0.699 | NA | NA |
| TSC2 | fluorouracil | 0.7001121 | 0.9561079 | 0.700 | NA | NA |
| G6PD | pazopanib | 0.7046983 | 0.9261994 | 0.7047 | NA | NA |
| KRAS | belinostat | 0.7060390 | 0.9332615 | 0.71 | NA | NA |
| PDGFRB | azd | 0.7069233 | 0.7511060 | 0.707 | NA | NA |
| BRCA2 | imatinib | 0.7069599 | 0.9654406 | 0.7070 | NA | NA |
| BRCA1 | vandetanib | 0.7073522 | 0.8720434 | 0.7074 | NA | NA |
| UGT1A1 | erlotinib | 0.7111266 | 0.9491271 | 0.711 | NA | NA |
| FLT3 | gefitinib | 0.7182420 | 0.8848141 | 0.718 | NA | NA |
| TSC1 | belinostat | 0.7219457 | 0.9332615 | 0.72 | NA | NA |
| ROS1 | vandetanib | 0.7251785 | 0.8720434 | 0.7252 | NA | NA |
| FLT3 | erlotinib | 0.7258031 | 0.9491271 | 0.726 | NA | NA |
| PDGFB | vandetanib | 0.7261157 | 0.8720434 | 0.7261 | NA | NA |
| MET | fluorouracil | 0.7280738 | 0.9561079 | 0.728 | NA | NA |
| FLT3 | trametinib | 0.7282232 | 0.8286678 | 0.7282 | NA | NA |
| ROS1 | ibrutinib | 0.7285250 | 0.9736731 | 0.7285 | NA | NA |
| PML | cyclophosphamide | 0.7303617 | 0.9793614 | 0.730 | NA | NA |
| TSC1 | ruxolitinib | 0.7316331 | 0.9851643 | 0.7316 | NA | NA |
| AKT1 | imatinib | 0.7320299 | 0.9654406 | 0.7320 | NA | NA |
| TSC2 | gefitinib | 0.7322403 | 0.8848141 | 0.732 | NA | NA |
| PTCH1 | afatinib | 0.7324281 | 0.8631215 | 0.7324 | NA | NA |
| ERBB3 | neratinib | 0.7332982 | 0.9509752 | 0.73330 | NA | NA |
| FLT3 | selumetinib | 0.7342484 | 0.8927666 | 0.73425 | NA | NA |
| ERBB3 | fluorouracil | 0.7345804 | 0.9561079 | 0.735 | NA | NA |
| ERBB2 | nilotinib | 0.7346282 | 0.8710739 | 0.735 | NA | NA |
| TSC1 | afatinib | 0.7361919 | 0.8631215 | 0.7362 | NA | NA |
| PDGFB | sunitinib | 0.7395816 | 0.9565998 | 0.73958 | NA | NA |
| PDGFRA | crizotinib | 0.7420103 | 0.9896386 | 0.742 | NA | NA |
| UGT1A1 | nilotinib | 0.7429748 | 0.8710739 | 0.743 | NA | NA |
| MGMT | selumetinib | 0.7434177 | 0.8927666 | 0.74342 | NA | NA |
| PML | vandetanib | 0.7438018 | 0.8720434 | 0.7438 | NA | NA |
| G6PD | olaparib | 0.7455081 | 0.9728161 | 0.74551 | NA | NA |
| BRCA2 | gefitinib | 0.7477970 | 0.8848141 | 0.748 | NA | NA |
| TSC2 | imatinib | 0.7480994 | 0.9654406 | 0.7481 | NA | NA |
| JAK2 | selumetinib | 0.7485902 | 0.8927666 | 0.74859 | NA | NA |
| DPYD | crizotinib | 0.7496551 | 0.9896386 | 0.750 | NA | NA |
| MYD88 | crizotinib | 0.7508273 | 0.9896386 | 0.751 | NA | NA |
| PDGFRB | dasatinib | 0.7535038 | 0.9367075 | 0.754 | NA | NA |
| PTCH1 | gefitinib | 0.7546944 | 0.8848141 | 0.755 | NA | NA |
| PDGFRB | dabrafenib | 0.7547325 | 0.9480461 | 0.75473 | NA | NA |
| NPM1 | olaparib | 0.7587867 | 0.9728161 | 0.75879 | NA | NA |
| G6PD | temozolomide | 0.7612249 | 0.9585795 | 0.761 | NA | NA |
| PDGFRB | lapatinib | 0.7618885 | 0.8634737 | 0.7619 | NA | NA |
| BRCA2 | regorafenib | 0.7635037 | 0.9410069 | 0.7635 | NA | NA |
| DPYD | imatinib | 0.7666734 | 0.9654406 | 0.7667 | NA | NA |
| TSC2 | olaparib | 0.7680842 | 0.9728161 | 0.76808 | NA | NA |
| EGFR | sunitinib | 0.7681397 | 0.9565998 | 0.76814 | NA | NA |
| DPYD | fluorouracil | 0.7693491 | 0.9561079 | 0.769 | NA | NA |
| FLT3 | sunitinib | 0.7714998 | 0.9565998 | 0.77150 | NA | NA |
| MYD88 | dasatinib | 0.7715129 | 0.9367075 | 0.772 | NA | NA |
| EGFR | fluorouracil | 0.7720863 | 0.9561079 | 0.772 | NA | NA |
| ERBB2 | ibrutinib | 0.7726805 | 0.9736731 | 0.7727 | NA | NA |
| PDGFRB | vandetanib | 0.7728525 | 0.8735853 | 0.7729 | NA | NA |
| TSC2 | belinostat | 0.7739206 | 0.9332615 | 0.77 | NA | NA |
| UGT1A1 | vemurafenib | 0.7774617 | 0.9065616 | 0.77746 | NA | NA |
| ESR1 | dasatinib | 0.7776986 | 0.9367075 | 0.778 | NA | NA |
| KIT | dasatinib | 0.7790279 | 0.9367075 | 0.779 | NA | NA |
| MYD88 | regorafenib | 0.7798439 | 0.9410069 | 0.7798 | NA | NA |
| ABL1 | dasatinib | 0.7801253 | 0.9367075 | 0.780 | NA | NA |
| ROS1 | dasatinib | 0.7804679 | 0.9367075 | 0.780 | NA | NA |
| BRCA1 | erlotinib | 0.7809136 | 0.9494085 | 0.781 | NA | NA |
| MYD88 | selumetinib | 0.7817427 | 0.8927666 | 0.78174 | NA | NA |
| RET | ibrutinib | 0.7824502 | 0.9736731 | 0.7825 | NA | NA |
| EGFR | belinostat | 0.7834615 | 0.9332615 | 0.78 | NA | NA |
| CYP19A1 | neratinib | 0.7845031 | 0.9509752 | 0.78450 | NA | NA |
| MET | belinostat | 0.7848683 | 0.9332615 | 0.78 | NA | NA |
| PDGFRB | cyclophosphamide | 0.7850095 | 0.9793614 | 0.785 | NA | NA |
| MGMT | cabozantinib | 0.7880782 | 0.8373331 | 0.7881 | NA | NA |
| BRCA1 | trametinib | 0.7902084 | 0.8422588 | 0.7902 | NA | NA |
| ALK | pazopanib | 0.7907566 | 0.9261994 | 0.7908 | NA | NA |
| NPM1 | trametinib | 0.7912128 | 0.8422588 | 0.7912 | NA | NA |
| MYD88 | sunitinib | 0.7948466 | 0.9565998 | 0.79485 | NA | NA |
| FLT3 | fluorouracil | 0.7949588 | 0.9561079 | 0.795 | NA | NA |
| BRCA2 | fulvestrant | 0.7961724 | 0.9582702 | 0.7962 | NA | NA |
| ESR1 | vandetanib | 0.7965042 | 0.8735853 | 0.7965 | NA | NA |
| IDH2 | belinostat | 0.7972643 | 0.9332615 | 0.80 | NA | NA |
| NPM1 | regorafenib | 0.8002281 | 0.9410069 | 0.8002 | NA | NA |
| ROS1 | dabrafenib | 0.8003190 | 0.9480461 | 0.80032 | NA | NA |
| CYP19A1 | erlotinib | 0.8021724 | 0.9494085 | 0.802 | NA | NA |
| TSC2 | dabrafenib | 0.8039511 | 0.9480461 | 0.80395 | NA | NA |
| ERBB2 | pazopanib | 0.8041509 | 0.9261994 | 0.8042 | NA | NA |
| EGFR | imatinib | 0.8043300 | 0.9690754 | 0.8043 | NA | NA |
| ERBB3 | vemurafenib | 0.8058873 | 0.9065616 | 0.80589 | NA | NA |
| IDH2 | gefitinib | 0.8069304 | 0.9145211 | 0.807 | NA | NA |
| AKT1 | fulvestrant | 0.8069482 | 0.9582702 | 0.8069 | NA | NA |
| TPMT | temozolomide | 0.8089661 | 0.9600068 | 0.809 | NA | NA |
| NPM1 | dasatinib | 0.8123866 | 0.9367075 | 0.812 | NA | NA |
| BRCA1 | olaparib | 0.8126710 | 0.9728161 | 0.81267 | NA | NA |
| FLT3 | afatinib | 0.8136811 | 0.9017076 | 0.8137 | NA | NA |
| TSC2 | pazopanib | 0.8156658 | 0.9261994 | 0.8157 | NA | NA |
| EGFR | selumetinib | 0.8175946 | 0.8927666 | 0.81759 | NA | NA |
| KRAS | fluorouracil | 0.8178870 | 0.9561079 | 0.818 | NA | NA |
| DNMT3A | dabrafenib | 0.8196290 | 0.9480461 | 0.81963 | NA | NA |
| KRAS | erlotinib | 0.8197849 | 0.9494085 | 0.820 | NA | NA |
| JAK2 | ruxolitinib | 0.8206972 | 0.9851643 | 0.8207 | NA | NA |
| ABL1 | neratinib | 0.8209775 | 0.9509752 | 0.82098 | NA | NA |
| JAK2 | pazopanib | 0.8212255 | 0.9261994 | 0.8212 | NA | NA |
| ESR1 | afatinib | 0.8221452 | 0.9017076 | 0.8221 | NA | NA |
| AKT1 | selumetinib | 0.8255265 | 0.8927666 | 0.82553 | NA | NA |
| ERBB3 | dasatinib | 0.8265066 | 0.9367075 | 0.827 | NA | NA |
| ERBB3 | regorafenib | 0.8265906 | 0.9410069 | 0.8266 | NA | NA |
| G6PD | belinostat | 0.8270727 | 0.9332615 | 0.83 | NA | NA |
| BRCA2 | sunitinib | 0.8280670 | 0.9565998 | 0.82807 | NA | NA |
| TSC2 | regorafenib | 0.8307456 | 0.9410069 | 0.8307 | NA | NA |
| ABL1 | dabrafenib | 0.8331314 | 0.9480461 | 0.83313 | NA | NA |
| JAK2 | imatinib | 0.8347277 | 0.9690754 | 0.8347 | NA | NA |
| ABL1 | pazopanib | 0.8358559 | 0.9261994 | 0.8359 | NA | NA |
| TPMT | nilotinib | 0.8378567 | 0.9337740 | 0.838 | NA | NA |
| BRCA2 | ruxolitinib | 0.8386749 | 0.9851643 | 0.8387 | NA | NA |
| TPMT | fulvestrant | 0.8400737 | 0.9582702 | 0.8401 | NA | NA |
| KIT | belinostat | 0.8435673 | 0.9332615 | 0.84 | NA | NA |
| ABL1 | sunitinib | 0.8440587 | 0.9565998 | 0.84406 | NA | NA |
| EGFR | cyclophosphamide | 0.8442118 | 0.9793614 | 0.844 | NA | NA |
| TPMT | belinostat | 0.8445547 | 0.9332615 | 0.84 | NA | NA |
| PDGFRB | erlotinib | 0.8448409 | 0.9494085 | 0.845 | NA | NA |
| PML | azd | 0.8448624 | 0.8704643 | 0.845 | NA | NA |
| PDGFB | fulvestrant | 0.8455325 | 0.9582702 | 0.8455 | NA | NA |
| DNMT3A | belinostat | 0.8463546 | 0.9332615 | 0.85 | NA | NA |
| ALK | cabozantinib | 0.8474970 | 0.8731787 | 0.8475 | NA | NA |
| JAK2 | belinostat | 0.8481782 | 0.9332615 | 0.85 | NA | NA |
| ESR1 | ruxolitinib | 0.8489985 | 0.9851643 | 0.8490 | NA | NA |
| MGMT | pazopanib | 0.8490601 | 0.9261994 | 0.8491 | NA | NA |
| PDGFB | afatinib | 0.8499921 | 0.9031166 | 0.8500 | NA | NA |
| BRCA1 | ibrutinib | 0.8510774 | 0.9736731 | 0.8511 | NA | NA |
| IDH2 | nilotinib | 0.8513822 | 0.9337740 | 0.851 | NA | NA |
| CYP19A1 | pazopanib | 0.8533966 | 0.9261994 | 0.8534 | NA | NA |
| PDGFRA | imatinib | 0.8550665 | 0.9690754 | 0.8551 | NA | NA |
| PDGFB | crizotinib | 0.8558808 | 0.9896386 | 0.856 | NA | NA |
| PTCH1 | neratinib | 0.8565156 | 0.9509752 | 0.85652 | NA | NA |
| G6PD | neratinib | 0.8580742 | 0.9509752 | 0.85807 | NA | NA |
| ERBB3 | temozolomide | 0.8609254 | 0.9600068 | 0.861 | NA | NA |
| FLT3 | neratinib | 0.8622113 | 0.9509752 | 0.86221 | NA | NA |
| ERBB3 | trametinib | 0.8637892 | 0.8907826 | 0.8638 | NA | NA |
| ROS1 | selumetinib | 0.8640047 | 0.8927666 | 0.86400 | NA | NA |
| MET | ruxolitinib | 0.8650705 | 0.9851643 | 0.8651 | NA | NA |
| TSC2 | selumetinib | 0.8665087 | 0.8927666 | 0.86651 | NA | NA |
| BRCA1 | cyclophosphamide | 0.8713387 | 0.9793614 | 0.871 | NA | NA |
| ALK | cyclophosphamide | 0.8716671 | 0.9793614 | 0.872 | NA | NA |
| ERBB2 | regorafenib | 0.8725903 | 0.9410069 | 0.8726 | NA | NA |
| EGFR | temozolomide | 0.8736252 | 0.9600068 | 0.874 | NA | NA |
| PML | ibrutinib | 0.8740839 | 0.9736731 | 0.8741 | NA | NA |
| MET | ibrutinib | 0.8773082 | 0.9736731 | 0.8773 | NA | NA |
| G6PD | erlotinib | 0.8787499 | 0.9494085 | 0.879 | NA | NA |
| PDGFB | cabozantinib | 0.8796954 | 0.8796954 | 0.8797 | NA | NA |
| BRCA1 | ruxolitinib | 0.8813093 | 0.9851643 | 0.8813 | NA | NA |
| ERBB3 | olaparib | 0.8819557 | 0.9728161 | 0.88196 | NA | NA |
| NPM1 | vemurafenib | 0.8824014 | 0.9065616 | 0.88240 | NA | NA |
| ESR1 | pazopanib | 0.8825243 | 0.9261994 | 0.8825 | NA | NA |
| ABL1 | vemurafenib | 0.8828642 | 0.9065616 | 0.88286 | NA | NA |
| KIT | vemurafenib | 0.8838594 | 0.9065616 | 0.88386 | NA | NA |
| BRAF | crizotinib | 0.8847422 | 0.9896386 | 0.885 | NA | NA |
| MGMT | regorafenib | 0.8856536 | 0.9410069 | 0.8857 | NA | NA |
| FLT3 | azd | 0.8863568 | 0.8863568 | 0.886 | NA | NA |
| TSC2 | fulvestrant | 0.8866945 | 0.9688694 | 0.8867 | NA | NA |
| RET | temozolomide | 0.8870447 | 0.9600068 | 0.887 | NA | NA |
| EGFR | gefitinib | 0.8875800 | 0.9734748 | 0.888 | NA | NA |
| MET | dasatinib | 0.8890135 | 0.9662257 | 0.889 | NA | NA |
| PML | neratinib | 0.8916365 | 0.9509752 | 0.89164 | NA | NA |
| ABL1 | erlotinib | 0.8935609 | 0.9494085 | 0.894 | NA | NA |
| KIT | nilotinib | 0.8943017 | 0.9501956 | 0.894 | NA | NA |
| MGMT | ibrutinib | 0.8947146 | 0.9736731 | 0.8947 | NA | NA |
| JAK2 | lapatinib | 0.8953005 | 0.9427410 | 0.8953 | NA | NA |
| MET | imatinib | 0.8955374 | 0.9790505 | 0.8955 | NA | NA |
| ERBB2 | lapatinib | 0.8966122 | 0.9427410 | 0.8966 | NA | NA |
| BRCA2 | fluorouracil | 0.8966696 | 0.9561079 | 0.897 | NA | NA |
| MYD88 | belinostat | 0.8969609 | 0.9332615 | 0.90 | NA | NA |
| CYP19A1 | crizotinib | 0.8996262 | 0.9896386 | 0.900 | NA | NA |
| IDH2 | sunitinib | 0.9001651 | 0.9857115 | 0.90017 | NA | NA |
| FLT3 | cyclophosphamide | 0.9009165 | 0.9793614 | 0.901 | NA | NA |
| NPM1 | belinostat | 0.9011013 | 0.9332615 | 0.90 | NA | NA |
| IDH2 | temozolomide | 0.9035358 | 0.9600068 | 0.904 | NA | NA |
| TPMT | vemurafenib | 0.9065616 | 0.9065616 | 0.90656 | NA | NA |
| ESR1 | crizotinib | 0.9085657 | 0.9896386 | 0.909 | NA | NA |
| JAK2 | dasatinib | 0.9093889 | 0.9662257 | 0.909 | NA | NA |
| ESR1 | cyclophosphamide | 0.9094059 | 0.9793614 | 0.909 | NA | NA |
| RET | olaparib | 0.9112727 | 0.9728161 | 0.91127 | NA | NA |
| DNMT3A | fulvestrant | 0.9118771 | 0.9688694 | 0.9119 | NA | NA |
| PTCH1 | vandetanib | 0.9121958 | 0.9305740 | 0.9122 | NA | NA |
| JAK2 | fluorouracil | 0.9122887 | 0.9561079 | 0.912 | NA | NA |
| PTCH1 | ruxolitinib | 0.9145576 | 0.9851643 | 0.9146 | NA | NA |
| PDGFB | lapatinib | 0.9150133 | 0.9427410 | 0.9150 | NA | NA |
| AKT1 | dabrafenib | 0.9165171 | 0.9896121 | 0.91652 | NA | NA |
| DPYD | pazopanib | 0.9171346 | 0.9261994 | 0.9171 | NA | NA |
| ROS1 | fluorouracil | 0.9179969 | 0.9561079 | 0.918 | NA | NA |
| PDGFRA | olaparib | 0.9187781 | 0.9728161 | 0.91878 | NA | NA |
| EGFR | neratinib | 0.9192244 | 0.9509752 | 0.91922 | NA | NA |
| PTCH1 | cyclophosphamide | 0.9194906 | 0.9793614 | 0.919 | NA | NA |
| TSC2 | ibrutinib | 0.9206937 | 0.9736731 | 0.9207 | NA | NA |
| PDGFB | cyclophosphamide | 0.9213531 | 0.9793614 | 0.921 | NA | NA |
| ESR1 | selumetinib | 0.9216779 | 0.9216779 | 0.92168 | NA | NA |
| MYD88 | cyclophosphamide | 0.9220687 | 0.9793614 | 0.922 | NA | NA |
| CYP19A1 | trametinib | 0.9221480 | 0.9221480 | 0.9221 | NA | NA |
| UGT1A1 | belinostat | 0.9223455 | 0.9332615 | 0.92 | NA | NA |
| JAK2 | neratinib | 0.9230054 | 0.9509752 | 0.92301 | NA | NA |
| ESR1 | belinostat | 0.9247735 | 0.9332615 | 0.92 | NA | NA |
| PDGFRA | belinostat | 0.9258624 | 0.9332615 | 0.93 | NA | NA |
| EGFR | pazopanib | 0.9261994 | 0.9261994 | 0.9262 | NA | NA |
| BRCA2 | nilotinib | 0.9267694 | 0.9548533 | 0.927 | NA | NA |
| UGT1A1 | vandetanib | 0.9276534 | 0.9305740 | 0.9277 | NA | NA |
| FLT3 | vandetanib | 0.9305740 | 0.9305740 | 0.9306 | NA | NA |
| AKT1 | belinostat | 0.9332615 | 0.9332615 | 0.93 | NA | NA |
| BRCA1 | afatinib | 0.9350732 | 0.9634087 | 0.9351 | NA | NA |
| ERBB3 | ibrutinib | 0.9351931 | 0.9736731 | 0.9352 | NA | NA |
| IDH2 | ibrutinib | 0.9361769 | 0.9736731 | 0.9362 | NA | NA |
| EGFR | crizotinib | 0.9363173 | 0.9896386 | 0.936 | NA | NA |
| IDH2 | fluorouracil | 0.9380996 | 0.9561079 | 0.938 | NA | NA |
| MYD88 | olaparib | 0.9407553 | 0.9728161 | 0.94076 | NA | NA |
| ERBB2 | sunitinib | 0.9415781 | 0.9857115 | 0.94158 | NA | NA |
| FLT3 | ruxolitinib | 0.9427873 | 0.9851643 | 0.9428 | NA | NA |
| IDH2 | regorafenib | 0.9449361 | 0.9661684 | 0.9449 | NA | NA |
| CYP19A1 | gefitinib | 0.9492185 | 0.9871832 | 0.949 | NA | NA |
| ROS1 | neratinib | 0.9510033 | 0.9510033 | 0.95100 | NA | NA |
| NPM1 | imatinib | 0.9542718 | 0.9790505 | 0.9543 | NA | NA |
| KIT | fluorouracil | 0.9561079 | 0.9561079 | 0.956 | NA | NA |
| G6PD | ruxolitinib | 0.9561889 | 0.9851643 | 0.9562 | NA | NA |
| PDGFRB | olaparib | 0.9563573 | 0.9728161 | 0.95636 | NA | NA |
| ABL1 | lapatinib | 0.9564785 | 0.9564785 | 0.9565 | NA | NA |
| ALK | sunitinib | 0.9567200 | 0.9857115 | 0.95672 | NA | NA |
| PDGFB | temozolomide | 0.9628530 | 0.9895199 | 0.963 | NA | NA |
| MYD88 | erlotinib | 0.9646182 | 0.9832344 | 0.965 | NA | NA |
| PTCH1 | ibrutinib | 0.9649617 | 0.9736731 | 0.9650 | NA | NA |
| TSC1 | cyclophosphamide | 0.9655074 | 0.9793614 | 0.966 | NA | NA |
| ESR1 | dabrafenib | 0.9659108 | 0.9896121 | 0.96591 | NA | NA |
| DNMT3A | regorafenib | 0.9661684 | 0.9661684 | 0.9662 | NA | NA |
| BRCA1 | dabrafenib | 0.9666621 | 0.9896121 | 0.96666 | NA | NA |
| KIT | fulvestrant | 0.9667212 | 0.9765345 | 0.9667 | NA | NA |
| ERBB2 | olaparib | 0.9669476 | 0.9728161 | 0.96695 | NA | NA |
| AKT1 | nilotinib | 0.9672155 | 0.9672155 | 0.967 | NA | NA |
| ROS1 | imatinib | 0.9684583 | 0.9790505 | 0.9685 | NA | NA |
| ERBB2 | crizotinib | 0.9689644 | 0.9896386 | 0.969 | NA | NA |
| TSC1 | gefitinib | 0.9708568 | 0.9871832 | 0.971 | NA | NA |
| DPYD | olaparib | 0.9728161 | 0.9728161 | 0.97282 | NA | NA |
| DPYD | ibrutinib | 0.9736731 | 0.9736731 | 0.9737 | NA | NA |
| G6PD | crizotinib | 0.9756109 | 0.9896386 | 0.976 | NA | NA |
| UGT1A1 | fulvestrant | 0.9765345 | 0.9765345 | 0.9765 | NA | NA |
| DPYD | dasatinib | 0.9779403 | 0.9980158 | 0.978 | NA | NA |
| G6PD | imatinib | 0.9790505 | 0.9790505 | 0.9791 | NA | NA |
| PDGFRA | cyclophosphamide | 0.9793614 | 0.9793614 | 0.979 | NA | NA |
| ERBB3 | erlotinib | 0.9832344 | 0.9832344 | 0.983 | NA | NA |
| BRAF | gefitinib | 0.9871832 | 0.9871832 | 0.987 | NA | NA |
| BRCA1 | crizotinib | 0.9886434 | 0.9896386 | 0.989 | NA | NA |
| KIT | temozolomide | 0.9895199 | 0.9895199 | 0.990 | NA | NA |
| RET | dabrafenib | 0.9896121 | 0.9896121 | 0.98961 | NA | NA |
| FLT3 | crizotinib | 0.9896386 | 0.9896386 | 0.990 | NA | NA |
| BRAF | sunitinib | 0.9897961 | 0.9897961 | 0.98980 | NA | NA |
| NPM1 | afatinib | 0.9954026 | 0.9954026 | 0.9954 | NA | NA |
| KIT | ruxolitinib | 0.9977843 | 0.9977843 | 0.9978 | NA | NA |
| UGT1A1 | dasatinib | 0.9980158 | 0.9980158 | 0.998 | NA | NA |
gdsc_signif_g2p <- compare_means(AUC ~ Mutation_Status_Nonsilent, group.by = "Drug_Gene", data = gdsc_data_g2p, method = "wilcox.test", p.adjust.method = "BH")
gdsc_signif_g2p <- adj_signif(gdsc_signif_g2p)
gdsc_signif_g2p <- gdsc_signif_g2p[order(gdsc_signif_g2p$p),]
saveRDS(gdsc_signif_g2p, "./data_munging/rds/gdsc_signif_g2p_gene.rds")
gdsc_signif_g2p_ByDrug <- lapply(unique(gdsc_data_g2p_genesfilt$Drug), WilcoxonByDrug, dataset = gdsc_data_g2p_genesfilt, data_name = "gdsc")
names(gdsc_signif_g2p_ByDrug) <- unique(gdsc_data_g2p_genesfilt$Drug)
saveRDS(gdsc_signif_g2p_ByDrug, "./data_munging/rds/gdsc_signif_g2p_ByDrug.rds")
gdsc_signif_g2p <- readRDS("./data_munging/rds/gdsc_signif_g2p_gene.rds")
knitr::kable(gdsc_signif_g2p[, c("Drug_Gene", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "GDSC: Wilcoxon test results for Level A point mutations, p < 0.01 (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Drug_Gene | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|
| dabrafenib_BRAF | 0.0001234 | 0.0034674 | 0.00012 | *** | ** |
| trametinib_BRAF | 0.0001576 | 0.0034674 | 0.00016 | *** | ** |
| afatinib_ERBB2 | 0.0171962 | 0.2522113 | 0.01720 |
|
NA |
| ponatinib_ABL1 | 0.0614896 | 0.6763861 | 0.06149 | NA | NA |
| lapatinib_ERBB2 | 0.1230985 | 0.8133548 | 0.12310 | NA | NA |
| erlotinib_MET | 0.1281272 | 0.8133548 | 0.12813 | NA | NA |
| crizotinib_MET | 0.1305419 | 0.8133548 | 0.13054 | NA | NA |
| gefitinib_EGFR | 0.1651667 | 0.8133548 | 0.16517 | NA | NA |
| afatinib_KRAS | 0.1838668 | 0.8133548 | 0.18387 | NA | NA |
| alectinib_ROS1 | 0.2335276 | 0.8133548 | 0.23353 | NA | NA |
| dabrafenib_G6PD | 0.2443393 | 0.8133548 | 0.24434 | NA | NA |
| imatinib_PDGFB | 0.2502352 | 0.8133548 | 0.25024 | NA | NA |
| rucaparib_BRCA2 | 0.3140675 | 0.8133548 | 0.31407 | NA | NA |
| imatinib_PDGFRA | 0.3143676 | 0.8133548 | 0.31437 | NA | NA |
| crizotinib_ALK | 0.3700920 | 0.8133548 | 0.37009 | NA | NA |
| gefitinib_MET | 0.3977576 | 0.8133548 | 0.39776 | NA | NA |
| pazopanib_UGT1A1 | 0.3984406 | 0.8133548 | 0.39844 | NA | NA |
| belinostat_UGT1A1 | 0.4041103 | 0.8133548 | 0.40411 | NA | NA |
| tretinoin_PML | 0.4081601 | 0.8133548 | 0.40816 | NA | NA |
| dasatinib_ABL1 | 0.4250747 | 0.8133548 | 0.42507 | NA | NA |
| afatinib_EGFR | 0.4594260 | 0.8133548 | 0.45943 | NA | NA |
| imatinib_ABL1 | 0.4679914 | 0.8133548 | 0.46799 | NA | NA |
| imatinib_PDGFRB | 0.4699331 | 0.8133548 | 0.46993 | NA | NA |
| erlotinib_KRAS | 0.4886809 | 0.8133548 | 0.48868 | NA | NA |
| nilotinib_UGT1A1 | 0.4918297 | 0.8133548 | 0.49183 | NA | NA |
| sunitinib_PDGFRA | 0.4989956 | 0.8133548 | 0.49900 | NA | NA |
| cabozantinib_RET | 0.4991041 | 0.8133548 | 0.49910 | NA | NA |
| afatinib_ERBB3 | 0.5614904 | 0.8250718 | 0.56149 | NA | NA |
| rucaparib_BRCA1 | 0.5768966 | 0.8250718 | 0.57690 | NA | NA |
| gefitinib_KRAS | 0.6235545 | 0.8250718 | 0.62355 | NA | NA |
| lapatinib_KRAS | 0.6456344 | 0.8250718 | 0.64563 | NA | NA |
| midostaurin_FLT3 | 0.6526579 | 0.8250718 | 0.65266 | NA | NA |
| sunitinib_KIT | 0.6583214 | 0.8250718 | 0.65832 | NA | NA |
| temozolomide_MGMT | 0.6634570 | 0.8250718 | 0.66346 | NA | NA |
| alectinib_ALK | 0.6916060 | 0.8250718 | 0.69161 | NA | NA |
| docetaxel_ERBB2 | 0.7052502 | 0.8250718 | 0.70525 | NA | NA |
| palbociclib_ERBB2 | 0.7083268 | 0.8250718 | 0.70833 | NA | NA |
| vismodegib_PTCH1 | 0.7198241 | 0.8250718 | 0.71982 | NA | NA |
| nilotinib_ABL1 | 0.7313136 | 0.8250718 | 0.73131 | NA | NA |
| imatinib_KIT | 0.7505218 | 0.8255740 | 0.75052 | NA | NA |
| bosutinib monohydrate_ABL1 | 0.7708229 | 0.8272245 | 0.77082 | NA | NA |
| ruxolitinib_JAK2 | 0.8523436 | 0.8929314 | 0.85234 | NA | NA |
| crizotinib_ROS1 | 0.9055984 | 0.9218958 | 0.90560 | NA | NA |
| erlotinib_EGFR | 0.9218958 | 0.9218958 | 0.92190 | NA | NA |
gdsc_signif_g2p_ByDrug <- readRDS("./data_munging/rds/gdsc_signif_g2p_ByDrug.rds")
gdsc_signif_g2p_ByDrug_all <- rbindlist(gdsc_signif_g2p_ByDrug, use.names = TRUE)
gdsc_signif_g2p_ByDrug_all <- gdsc_signif_g2p_ByDrug_all[order(gdsc_signif_g2p_ByDrug_all$p),]
knitr::kable(gdsc_signif_g2p_ByDrug_all[, c("Hugo_Symbol", "Drug", "p", "p.adj", "p.format", "p.signif", "p.signif.adj")], caption = "GDSC: by-drug Wilcoxon test results for Level A point mutations, (BH-adjusted p-values: * p <= 0.05, ** p <= 0.01, *** p <= 0.001, **** p <= 0.0001)") %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>% scroll_box(width = "900px", height = "450px")
| Hugo_Symbol | Drug | p | p.adj | p.format | p.signif | p.signif.adj |
|---|---|---|---|---|---|---|
| KRAS | trametinib | 0.0000000 | 0.0000003 | 8.5e-09 | **** | **** |
| BRAF | dabrafenib | 0.0001234 | 0.0041947 | 0.00012 | *** | ** |
| BRAF | trametinib | 0.0001576 | 0.0026794 | 0.00016 | *** | ** |
| PDGFRB | cabozantinib | 0.0005036 | 0.0171218 | 0.0005 | *** |
|
| KRAS | palbociclib | 0.0017081 | 0.0580770 | 0.0017 | ** | NA |
| PDGFRB | tretinoin | 0.0032063 | 0.1090147 | 0.0032 | ** | NA |
| ROS1 | cabozantinib | 0.0037056 | 0.0629948 | 0.0037 | ** | NA |
| KRAS | pazopanib | 0.0043870 | 0.1308570 | 0.0044 | ** | NA |
| BRCA2 | midostaurin | 0.0058907 | 0.2002841 | 0.0059 | ** | NA |
| TSC1 | temozolomide | 0.0073262 | 0.2490920 | 0.0073 | ** | NA |
| ABL1 | pazopanib | 0.0076975 | 0.1308570 | 0.0077 | ** | NA |
| ALK | palbociclib | 0.0089754 | 0.1525816 | 0.0090 | ** | NA |
| ROS1 | trametinib | 0.0160528 | 0.1819317 | 0.01605 |
|
NA |
| DNMT3A | temozolomide | 0.0163008 | 0.2771142 | 0.0163 |
|
NA |
| BRCA1 | tretinoin | 0.0170421 | 0.2897149 | 0.0170 |
|
NA |
| ERBB2 | afatinib | 0.0171962 | 0.5609625 | 0.017 |
|
NA |
| BRAF | bosutinib monohydrate | 0.0181741 | 0.3173957 | 0.018 |
|
NA |
| KIT | bosutinib monohydrate | 0.0186703 | 0.3173957 | 0.019 |
|
NA |
| ABL1 | gefitinib | 0.0196537 | 0.6682274 | 0.020 |
|
NA |
| BRCA2 | erlotinib | 0.0208851 | 0.6683217 | 0.021 |
|
NA |
| DPYD | lapatinib | 0.0212882 | 0.6812223 | 0.021 |
|
NA |
| TPMT | cabozantinib | 0.0218657 | 0.2413818 | 0.0219 |
|
NA |
| MGMT | docetaxel | 0.0241785 | 0.6845085 | 0.024 |
|
NA |
| UGT1A1 | trametinib | 0.0274916 | 0.2336787 | 0.02749 |
|
NA |
| KRAS | dabrafenib | 0.0278924 | 0.3904427 | 0.02789 |
|
NA |
| FLT3 | cabozantinib | 0.0283979 | 0.2413818 | 0.0284 |
|
NA |
| TSC1 | sunitinib | 0.0300384 | 0.5453213 | 0.030 |
|
NA |
| ERBB3 | ponatinib | 0.0344904 | 0.9972326 | 0.034 |
|
NA |
| NPM1 | tretinoin | 0.0355459 | 0.3525943 | 0.0355 |
|
NA |
| JAK2 | dabrafenib | 0.0362699 | 0.3904427 | 0.03627 |
|
NA |
| FLT3 | crizotinib | 0.0371049 | 0.3575404 | 0.037 |
|
NA |
| UGT1A1 | afatinib | 0.0384529 | 0.5609625 | 0.038 |
|
NA |
| UGT1A1 | midostaurin | 0.0385592 | 0.6011299 | 0.0386 |
|
NA |
| ERBB3 | temozolomide | 0.0387034 | 0.4275924 | 0.0387 |
|
NA |
| ESR1 | imatinib | 0.0394429 | 0.7846892 | 0.039 |
|
NA |
| TSC1 | crizotinib | 0.0396633 | 0.3575404 | 0.040 |
|
NA |
| BRCA2 | crizotinib | 0.0408902 | 0.3575404 | 0.041 |
|
NA |
| TSC1 | tretinoin | 0.0414817 | 0.3525943 | 0.0415 |
|
NA |
| ABL1 | cabozantinib | 0.0433477 | 0.2947646 | 0.0433 |
|
NA |
| DNMT3A | sunitinib | 0.0480660 | 0.5453213 | 0.048 |
|
NA |
| TPMT | temozolomide | 0.0503050 | 0.4275924 | 0.0503 | NA | NA |
| TSC1 | rucaparib | 0.0503265 | 0.8376438 | 0.050 | NA | NA |
| NPM1 | dabrafenib | 0.0506987 | 0.3904427 | 0.05070 | NA | NA |
| ABL1 | afatinib | 0.0507264 | 0.5609625 | 0.051 | NA | NA |
| KIT | nilotinib | 0.0509383 | 0.7074000 | 0.051 | NA | NA |
| RET | sunitinib | 0.0511239 | 0.5453213 | 0.051 | NA | NA |
| ERBB3 | dabrafenib | 0.0574180 | 0.3904427 | 0.05742 | NA | NA |
| TSC1 | bosutinib monohydrate | 0.0576889 | 0.6538081 | 0.058 | NA | NA |
| DNMT3A | crizotinib | 0.0577322 | 0.3575404 | 0.058 | NA | NA |
| PML | crizotinib | 0.0605225 | 0.3575404 | 0.061 | NA | NA |
| RET | alectinib | 0.0609957 | 0.6998836 | 0.061 | NA | NA |
| ABL1 | ponatinib | 0.0614896 | 0.9972326 | 0.061 | NA | NA |
| PDGFRA | alectinib | 0.0638924 | 0.6998836 | 0.064 | NA | NA |
| PTCH1 | cabozantinib | 0.0650780 | 0.3687756 | 0.0651 | NA | NA |
| PDGFB | ruxolitinib | 0.0653257 | 0.7847293 | 0.065 | NA | NA |
| TPMT | belinostat | 0.0656977 | 0.6734824 | 0.066 | NA | NA |
| ABL1 | ruxolitinib | 0.0661262 | 0.7847293 | 0.066 | NA | NA |
| PDGFRB | belinostat | 0.0666829 | 0.6734824 | 0.067 | NA | NA |
| CYP19A1 | ruxolitinib | 0.0692408 | 0.7847293 | 0.069 | NA | NA |
| DNMT3A | docetaxel | 0.0692678 | 0.6845085 | 0.069 | NA | NA |
| BRCA2 | lapatinib | 0.0716745 | 0.7620951 | 0.072 | NA | NA |
| KIT | trametinib | 0.0733706 | 0.4303556 | 0.07337 | NA | NA |
| TPMT | dabrafenib | 0.0737570 | 0.4179561 | 0.07376 | NA | NA |
| BRAF | belinostat | 0.0744959 | 0.6734824 | 0.074 | NA | NA |
| PDGFRB | dasatinib | 0.0763115 | 0.9447103 | 0.076 | NA | NA |
| DPYD | crizotinib | 0.0771266 | 0.3575404 | 0.077 | NA | NA |
| TSC1 | nilotinib | 0.0779898 | 0.7074000 | 0.078 | NA | NA |
| ERBB2 | crizotinib | 0.0782120 | 0.3575404 | 0.078 | NA | NA |
| ALK | gefitinib | 0.0794375 | 0.7564295 | 0.079 | NA | NA |
| FLT3 | erlotinib | 0.0848216 | 0.6714960 | 0.085 | NA | NA |
| AKT1 | nilotinib | 0.0856959 | 0.7074000 | 0.086 | NA | NA |
| PDGFRB | midostaurin | 0.0887296 | 0.6011299 | 0.0887 | NA | NA |
| JAK2 | trametinib | 0.0900127 | 0.4303556 | 0.09001 | NA | NA |
| UGT1A1 | tretinoin | 0.0911112 | 0.3862972 | 0.0911 | NA | NA |
| BRCA2 | tretinoin | 0.0916313 | 0.3862972 | 0.0916 | NA | NA |
| ABL1 | docetaxel | 0.0918631 | 0.6845085 | 0.092 | NA | NA |
| BRCA2 | dasatinib | 0.0931223 | 0.9447103 | 0.093 | NA | NA |
| IDH2 | cabozantinib | 0.0934140 | 0.4267811 | 0.0934 | NA | NA |
| TPMT | alectinib | 0.0935866 | 0.6998836 | 0.094 | NA | NA |
| ROS1 | erlotinib | 0.0943399 | 0.6714960 | 0.094 | NA | NA |
| MYD88 | ruxolitinib | 0.0954788 | 0.8115699 | 0.095 | NA | NA |
| NPM1 | dasatinib | 0.0957018 | 0.9447103 | 0.096 | NA | NA |
| TPMT | tretinoin | 0.0957413 | 0.3862972 | 0.0957 | NA | NA |
| MET | lapatinib | 0.0972319 | 0.7620951 | 0.097 | NA | NA |
| DNMT3A | rucaparib | 0.0975186 | 0.8376438 | 0.098 | NA | NA |
| RET | palbociclib | 0.0983382 | 0.7307299 | 0.0983 | NA | NA |
| ERBB2 | gefitinib | 0.0989296 | 0.7564295 | 0.099 | NA | NA |
| FLT3 | imatinib | 0.0990080 | 0.7846892 | 0.099 | NA | NA |
| JAK2 | cabozantinib | 0.1004191 | 0.4267811 | 0.1004 | NA | NA |
| BRCA2 | palbociclib | 0.1027690 | 0.7307299 | 0.1028 | NA | NA |
| MYD88 | trametinib | 0.1042757 | 0.4303556 | 0.10428 | NA | NA |
| PML | midostaurin | 0.1046555 | 0.6011299 | 0.1047 | NA | NA |
| TSC2 | tretinoin | 0.1061419 | 0.3862972 | 0.1061 | NA | NA |
| ABL1 | trametinib | 0.1069974 | 0.4303556 | 0.10700 | NA | NA |
| PDGFRA | gefitinib | 0.1077698 | 0.7564295 | 0.108 | NA | NA |
| CYP19A1 | imatinib | 0.1086620 | 0.7846892 | 0.109 | NA | NA |
| ERBB3 | midostaurin | 0.1104412 | 0.6011299 | 0.1104 | NA | NA |
| TSC2 | dabrafenib | 0.1118016 | 0.4630570 | 0.11180 | NA | NA |
| BRAF | palbociclib | 0.1131136 | 0.7307299 | 0.1131 | NA | NA |
| ROS1 | tretinoin | 0.1136424 | 0.3862972 | 0.1136 | NA | NA |
| ROS1 | ponatinib | 0.1143242 | 0.9972326 | 0.114 | NA | NA |
| ESR1 | temozolomide | 0.1154649 | 0.6370529 | 0.1155 | NA | NA |
| G6PD | bosutinib monohydrate | 0.1162560 | 0.8517410 | 0.116 | NA | NA |
| BRCA2 | imatinib | 0.1174800 | 0.7846892 | 0.117 | NA | NA |
| PDGFRA | tretinoin | 0.1216752 | 0.3862972 | 0.1217 | NA | NA |
| MGMT | afatinib | 0.1228036 | 0.5609625 | 0.123 | NA | NA |
| ERBB2 | lapatinib | 0.1230985 | 0.7620951 | 0.123 | NA | NA |
| TPMT | ruxolitinib | 0.1231531 | 0.8374409 | 0.123 | NA | NA |
| ERBB2 | midostaurin | 0.1231748 | 0.6011299 | 0.1232 | NA | NA |
| IDH2 | belinostat | 0.1232427 | 0.6734824 | 0.123 | NA | NA |
| KIT | tretinoin | 0.1249785 | 0.3862972 | 0.1250 | NA | NA |
| UGT1A1 | bosutinib monohydrate | 0.1252560 | 0.8517410 | 0.125 | NA | NA |
| ALK | dabrafenib | 0.1254923 | 0.4630570 | 0.12549 | NA | NA |
| MYD88 | docetaxel | 0.1258052 | 0.6845085 | 0.126 | NA | NA |
| MGMT | gefitinib | 0.1263998 | 0.7564295 | 0.126 | NA | NA |
| PTCH1 | midostaurin | 0.1266216 | 0.6011299 | 0.1266 | NA | NA |
| MET | erlotinib | 0.1281272 | 0.6714960 | 0.128 | NA | NA |
| MGMT | erlotinib | 0.1288089 | 0.6714960 | 0.129 | NA | NA |
| MET | crizotinib | 0.1305419 | 0.5221677 | 0.131 | NA | NA |
| ERBB2 | temozolomide | 0.1311049 | 0.6370529 | 0.1311 | NA | NA |
| IDH2 | temozolomide | 0.1311580 | 0.6370529 | 0.1312 | NA | NA |
| TSC2 | nilotinib | 0.1328358 | 0.7074000 | 0.133 | NA | NA |
| PDGFRA | afatinib | 0.1332170 | 0.5609625 | 0.133 | NA | NA |
| PTCH1 | gefitinib | 0.1346354 | 0.7564295 | 0.135 | NA | NA |
| PDGFRA | nilotinib | 0.1346957 | 0.7074000 | 0.135 | NA | NA |
| MET | belinostat | 0.1348014 | 0.6734824 | 0.135 | NA | NA |
| EGFR | dabrafenib | 0.1350723 | 0.4630570 | 0.13507 | NA | NA |
| PDGFRA | trametinib | 0.1350935 | 0.4303556 | 0.13509 | NA | NA |
| MET | dabrafenib | 0.1361932 | 0.4630570 | 0.13619 | NA | NA |
| JAK2 | vismodegib | 0.1385135 | 0.8104430 | 0.14 | NA | NA |
| ALK | trametinib | 0.1385711 | 0.4303556 | 0.13857 | NA | NA |
| TSC2 | trametinib | 0.1392327 | 0.4303556 | 0.13923 | NA | NA |
| PDGFRA | cabozantinib | 0.1407290 | 0.4442478 | 0.1407 | NA | NA |
| UGT1A1 | lapatinib | 0.1409522 | 0.7620951 | 0.141 | NA | NA |
| BRAF | rucaparib | 0.1413053 | 0.8376438 | 0.141 | NA | NA |
| AKT1 | midostaurin | 0.1419954 | 0.6011299 | 0.1420 | NA | NA |
| ALK | lapatinib | 0.1428928 | 0.7620951 | 0.143 | NA | NA |
| KIT | cabozantinib | 0.1434514 | 0.4442478 | 0.1435 | NA | NA |
| KRAS | cabozantinib | 0.1437272 | 0.4442478 | 0.1437 | NA | NA |
| PDGFB | erlotinib | 0.1449924 | 0.6714960 | 0.145 | NA | NA |
| ERBB3 | imatinib | 0.1453832 | 0.7846892 | 0.145 | NA | NA |
| UGT1A1 | erlotinib | 0.1468898 | 0.6714960 | 0.147 | NA | NA |
| RET | docetaxel | 0.1477981 | 0.6845085 | 0.148 | NA | NA |
| G6PD | alectinib | 0.1491983 | 0.6998836 | 0.149 | NA | NA |
| NPM1 | belinostat | 0.1498150 | 0.6734824 | 0.150 | NA | NA |
| IDH2 | rucaparib | 0.1502920 | 0.8376438 | 0.150 | NA | NA |
| MET | imatinib | 0.1511805 | 0.7846892 | 0.151 | NA | NA |
| AKT1 | bosutinib monohydrate | 0.1516806 | 0.8595235 | 0.152 | NA | NA |
| BRAF | alectinib | 0.1526449 | 0.6998836 | 0.153 | NA | NA |
| FLT3 | nilotinib | 0.1535908 | 0.7074000 | 0.154 | NA | NA |
| TSC2 | afatinib | 0.1594651 | 0.5609625 | 0.159 | NA | NA |
| BRAF | vismodegib | 0.1624273 | 0.8104430 | 0.16 | NA | NA |
| IDH2 | afatinib | 0.1625545 | 0.5609625 | 0.163 | NA | NA |
| TSC2 | temozolomide | 0.1628876 | 0.6854745 | 0.1629 | NA | NA |
| EGFR | gefitinib | 0.1651667 | 0.7564295 | 0.165 | NA | NA |
| BRCA1 | midostaurin | 0.1683042 | 0.6011299 | 0.1683 | NA | NA |
| ROS1 | docetaxel | 0.1704250 | 0.6845085 | 0.170 | NA | NA |
| TSC1 | trametinib | 0.1714196 | 0.4856889 | 0.17142 | NA | NA |
| PDGFB | tretinoin | 0.1722109 | 0.4533977 | 0.1722 | NA | NA |
| PTCH1 | tretinoin | 0.1733580 | 0.4533977 | 0.1734 | NA | NA |
| TSC2 | crizotinib | 0.1757036 | 0.6247240 | 0.176 | NA | NA |
| ESR1 | nilotinib | 0.1779167 | 0.7074000 | 0.178 | NA | NA |
| NPM1 | cabozantinib | 0.1781069 | 0.5046363 | 0.1781 | NA | NA |
| JAK2 | docetaxel | 0.1783666 | 0.6845085 | 0.178 | NA | NA |
| ERBB2 | belinostat | 0.1805478 | 0.6734824 | 0.181 | NA | NA |
| G6PD | docetaxel | 0.1822668 | 0.6845085 | 0.182 | NA | NA |
| MYD88 | afatinib | 0.1823685 | 0.5609625 | 0.182 | NA | NA |
| KRAS | afatinib | 0.1838668 | 0.5609625 | 0.184 | NA | NA |
| MET | afatinib | 0.1841947 | 0.5609625 | 0.184 | NA | NA |
| ABL1 | belinostat | 0.1850848 | 0.6734824 | 0.185 | NA | NA |
| DNMT3A | nilotinib | 0.1870610 | 0.7074000 | 0.187 | NA | NA |
| PTCH1 | bosutinib monohydrate | 0.1879013 | 0.8678254 | 0.188 | NA | NA |
| BRCA2 | alectinib | 0.1881297 | 0.6998836 | 0.188 | NA | NA |
| ALK | sunitinib | 0.1882759 | 0.8777619 | 0.188 | NA | NA |
| ALK | afatinib | 0.1885392 | 0.5609625 | 0.189 | NA | NA |
| TSC2 | sunitinib | 0.1886391 | 0.8777619 | 0.189 | NA | NA |
| PDGFRB | dabrafenib | 0.1895855 | 0.5719432 | 0.18959 | NA | NA |
| TSC1 | midostaurin | 0.1925940 | 0.6011299 | 0.1926 | NA | NA |
| NPM1 | imatinib | 0.1935911 | 0.7846892 | 0.194 | NA | NA |
| NPM1 | midostaurin | 0.1944832 | 0.6011299 | 0.1945 | NA | NA |
| MGMT | cabozantinib | 0.1946541 | 0.5090952 | 0.1947 | NA | NA |
| PML | alectinib | 0.1950849 | 0.6998836 | 0.195 | NA | NA |
| FLT3 | rucaparib | 0.1971116 | 0.8376438 | 0.197 | NA | NA |
| BRAF | ruxolitinib | 0.1976786 | 0.9414093 | 0.198 | NA | NA |
| TSC2 | docetaxel | 0.1988212 | 0.6845085 | 0.199 | NA | NA |
| JAK2 | gefitinib | 0.1997501 | 0.7564295 | 0.200 | NA | NA |
| ESR1 | gefitinib | 0.2002313 | 0.7564295 | 0.200 | NA | NA |
| UGT1A1 | palbociclib | 0.2007621 | 0.7307299 | 0.2008 | NA | NA |
| PML | palbociclib | 0.2018104 | 0.7307299 | 0.2018 | NA | NA |
| KIT | dabrafenib | 0.2027554 | 0.5719432 | 0.20276 | NA | NA |
| PDGFRB | erlotinib | 0.2028937 | 0.7675082 | 0.203 | NA | NA |
| IDH2 | vismodegib | 0.2041835 | 0.8104430 | 0.20 | NA | NA |
| TSC2 | ponatinib | 0.2051961 | 0.9972326 | 0.205 | NA | NA |
| FLT3 | dasatinib | 0.2059686 | 0.9447103 | 0.206 | NA | NA |
| JAK2 | temozolomide | 0.2108300 | 0.6854745 | 0.2108 | NA | NA |
| G6PD | afatinib | 0.2109900 | 0.5609625 | 0.211 | NA | NA |
| EGFR | crizotinib | 0.2113667 | 0.6763734 | 0.211 | NA | NA |
| ABL1 | palbociclib | 0.2122468 | 0.7307299 | 0.2122 | NA | NA |
| ESR1 | palbociclib | 0.2146985 | 0.7307299 | 0.2147 | NA | NA |
| NPM1 | erlotinib | 0.2158617 | 0.7675082 | 0.216 | NA | NA |
| PTCH1 | temozolomide | 0.2167760 | 0.6854745 | 0.2168 | NA | NA |
| ESR1 | belinostat | 0.2186179 | 0.6734824 | 0.219 | NA | NA |
| MYD88 | belinostat | 0.2195610 | 0.6734824 | 0.220 | NA | NA |
| BRCA1 | vismodegib | 0.2203270 | 0.8104430 | 0.22 | NA | NA |
| PML | temozolomide | 0.2217712 | 0.6854745 | 0.2218 | NA | NA |
| PDGFB | vismodegib | 0.2233811 | 0.8104430 | 0.22 | NA | NA |
| ROS1 | belinostat | 0.2235080 | 0.6734824 | 0.224 | NA | NA |
| KRAS | tretinoin | 0.2237016 | 0.5432753 | 0.2237 | NA | NA |
| NPM1 | alectinib | 0.2246258 | 0.6998836 | 0.225 | NA | NA |
| DNMT3A | dasatinib | 0.2260896 | 0.9447103 | 0.226 | NA | NA |
| ALK | ruxolitinib | 0.2294413 | 0.9414093 | 0.229 | NA | NA |
| PDGFB | afatinib | 0.2297013 | 0.5609625 | 0.230 | NA | NA |
| DPYD | ponatinib | 0.2315390 | 0.9972326 | 0.232 | NA | NA |
| G6PD | ruxolitinib | 0.2325984 | 0.9414093 | 0.233 | NA | NA |
| KIT | vismodegib | 0.2326739 | 0.8104430 | 0.23 | NA | NA |
| ROS1 | alectinib | 0.2335276 | 0.6998836 | 0.234 | NA | NA |
| ABL1 | lapatinib | 0.2342922 | 0.8759947 | 0.234 | NA | NA |
| PTCH1 | belinostat | 0.2376997 | 0.6734824 | 0.238 | NA | NA |
| JAK2 | alectinib | 0.2385373 | 0.6998836 | 0.239 | NA | NA |
| MGMT | palbociclib | 0.2389195 | 0.7307299 | 0.2389 | NA | NA |
| TSC2 | alectinib | 0.2393143 | 0.6998836 | 0.239 | NA | NA |
| CYP19A1 | trametinib | 0.2426959 | 0.5652949 | 0.24270 | NA | NA |
| G6PD | dabrafenib | 0.2443393 | 0.5719432 | 0.24434 | NA | NA |
| DPYD | trametinib | 0.2458254 | 0.5652949 | 0.24583 | NA | NA |
| G6PD | vismodegib | 0.2460143 | 0.8104430 | 0.25 | NA | NA |
| ABL1 | alectinib | 0.2470177 | 0.6998836 | 0.247 | NA | NA |
| TSC1 | vismodegib | 0.2476631 | 0.8104430 | 0.25 | NA | NA |
| IDH2 | bosutinib monohydrate | 0.2477175 | 0.8678254 | 0.248 | NA | NA |
| ERBB3 | tretinoin | 0.2487626 | 0.5613501 | 0.2488 | NA | NA |
| NPM1 | docetaxel | 0.2488101 | 0.6845085 | 0.249 | NA | NA |
| RET | trametinib | 0.2493948 | 0.5652949 | 0.24939 | NA | NA |
| KRAS | ponatinib | 0.2496849 | 0.9972326 | 0.250 | NA | NA |
| PDGFB | imatinib | 0.2502352 | 0.7846892 | 0.250 | NA | NA |
| MGMT | lapatinib | 0.2514271 | 0.8759947 | 0.251 | NA | NA |
| ERBB2 | dabrafenib | 0.2521562 | 0.5719432 | 0.25216 | NA | NA |
| PML | dabrafenib | 0.2532744 | 0.5719432 | 0.25327 | NA | NA |
| EGFR | dasatinib | 0.2539632 | 0.9447103 | 0.254 | NA | NA |
| BRCA1 | bosutinib monohydrate | 0.2550079 | 0.8678254 | 0.255 | NA | NA |
| BRCA2 | afatinib | 0.2553180 | 0.5609625 | 0.255 | NA | NA |
| PML | sunitinib | 0.2560406 | 0.8777619 | 0.256 | NA | NA |
| TSC2 | palbociclib | 0.2593090 | 0.7307299 | 0.2593 | NA | NA |
| IDH2 | ponatinib | 0.2610616 | 0.9972326 | 0.261 | NA | NA |
| PTCH1 | ponatinib | 0.2619913 | 0.9972326 | 0.262 | NA | NA |
| UGT1A1 | crizotinib | 0.2625570 | 0.7638022 | 0.263 | NA | NA |
| TPMT | docetaxel | 0.2626723 | 0.6845085 | 0.263 | NA | NA |
| PTCH1 | afatinib | 0.2628105 | 0.5609625 | 0.263 | NA | NA |
| PDGFB | lapatinib | 0.2633229 | 0.8759947 | 0.263 | NA | NA |
| DNMT3A | afatinib | 0.2639824 | 0.5609625 | 0.264 | NA | NA |
| TPMT | vismodegib | 0.2650075 | 0.8104430 | 0.27 | NA | NA |
| BRAF | docetaxel | 0.2666895 | 0.6845085 | 0.267 | NA | NA |
| MGMT | midostaurin | 0.2670503 | 0.7109289 | 0.2671 | NA | NA |
| DNMT3A | cabozantinib | 0.2687536 | 0.6476573 | 0.2688 | NA | NA |
| DPYD | dabrafenib | 0.2691497 | 0.5719432 | 0.26915 | NA | NA |
| JAK2 | tretinoin | 0.2702044 | 0.5613501 | 0.2702 | NA | NA |
| EGFR | alectinib | 0.2707820 | 0.7081991 | 0.271 | NA | NA |
| ALK | belinostat | 0.2712457 | 0.7094119 | 0.271 | NA | NA |
| AKT1 | vismodegib | 0.2724738 | 0.8104430 | 0.27 | NA | NA |
| KRAS | docetaxel | 0.2725554 | 0.6845085 | 0.273 | NA | NA |
| NPM1 | lapatinib | 0.2737483 | 0.8759947 | 0.274 | NA | NA |
| TPMT | nilotinib | 0.2737875 | 0.7074000 | 0.274 | NA | NA |
| PDGFRB | nilotinib | 0.2738696 | 0.7074000 | 0.274 | NA | NA |
| ERBB2 | trametinib | 0.2740267 | 0.5823067 | 0.27403 | NA | NA |
| NPM1 | temozolomide | 0.2747200 | 0.7783735 | 0.2747 | NA | NA |
| PDGFB | nilotinib | 0.2752114 | 0.7074000 | 0.275 | NA | NA |
| JAK2 | rucaparib | 0.2799799 | 0.8376438 | 0.280 | NA | NA |
| KIT | ruxolitinib | 0.2812051 | 0.9414093 | 0.281 | NA | NA |
| PDGFRB | docetaxel | 0.2818564 | 0.6845085 | 0.282 | NA | NA |
| PDGFRA | midostaurin | 0.2883532 | 0.7109289 | 0.2884 | NA | NA |
| ERBB3 | cabozantinib | 0.2887403 | 0.6476573 | 0.2887 | NA | NA |
| MET | palbociclib | 0.2900431 | 0.7307299 | 0.2900 | NA | NA |
| MET | vismodegib | 0.2900560 | 0.8104430 | 0.29 | NA | NA |
| BRCA2 | bosutinib monohydrate | 0.2907814 | 0.8678254 | 0.291 | NA | NA |
| KRAS | midostaurin | 0.2927354 | 0.7109289 | 0.2927 | NA | NA |
| PTCH1 | pazopanib | 0.2950783 | 0.9239682 | 0.2951 | NA | NA |
| AKT1 | alectinib | 0.2956410 | 0.7179852 | 0.296 | NA | NA |
| UGT1A1 | imatinib | 0.2957214 | 0.7846892 | 0.296 | NA | NA |
| ROS1 | bosutinib monohydrate | 0.2963370 | 0.8678254 | 0.296 | NA | NA |
| FLT3 | trametinib | 0.2977892 | 0.5955784 | 0.29779 | NA | NA |
| ERBB2 | tretinoin | 0.3012993 | 0.5613501 | 0.3013 | NA | NA |
| AKT1 | ruxolitinib | 0.3044779 | 0.9414093 | 0.304 | NA | NA |
| TSC1 | ruxolitinib | 0.3045736 | 0.9414093 | 0.305 | NA | NA |
| DPYD | cabozantinib | 0.3047799 | 0.6476573 | 0.3048 | NA | NA |
| IDH2 | pazopanib | 0.3050404 | 0.9239682 | 0.3050 | NA | NA |
| PTCH1 | nilotinib | 0.3093982 | 0.7074000 | 0.309 | NA | NA |
| BRAF | tretinoin | 0.3097622 | 0.5613501 | 0.3098 | NA | NA |
| DPYD | afatinib | 0.3107947 | 0.6215893 | 0.311 | NA | NA |
| TSC1 | imatinib | 0.3108496 | 0.7846892 | 0.311 | NA | NA |
| MGMT | rucaparib | 0.3112521 | 0.8376438 | 0.311 | NA | NA |
| TPMT | gefitinib | 0.3116629 | 0.8402334 | 0.312 | NA | NA |
| ERBB2 | dasatinib | 0.3121664 | 0.9447103 | 0.312 | NA | NA |
| MET | tretinoin | 0.3136957 | 0.5613501 | 0.3137 | NA | NA |
| BRCA2 | rucaparib | 0.3140675 | 0.8376438 | 0.314 | NA | NA |
| PDGFRA | imatinib | 0.3143676 | 0.7846892 | 0.314 | NA | NA |
| ESR1 | rucaparib | 0.3155348 | 0.8376438 | 0.316 | NA | NA |
| KRAS | belinostat | 0.3158051 | 0.7166062 | 0.316 | NA | NA |
| ERBB2 | imatinib | 0.3160344 | 0.7846892 | 0.316 | NA | NA |
| CYP19A1 | belinostat | 0.3161498 | 0.7166062 | 0.316 | NA | NA |
| KIT | rucaparib | 0.3176892 | 0.8376438 | 0.318 | NA | NA |
| PTCH1 | palbociclib | 0.3180803 | 0.7307299 | 0.3181 | NA | NA |
| NPM1 | nilotinib | 0.3197255 | 0.7074000 | 0.320 | NA | NA |
| ROS1 | rucaparib | 0.3210092 | 0.8376438 | 0.321 | NA | NA |
| DPYD | vismodegib | 0.3255816 | 0.8104430 | 0.33 | NA | NA |
| IDH2 | gefitinib | 0.3258316 | 0.8402334 | 0.326 | NA | NA |
| FLT3 | gefitinib | 0.3274937 | 0.8402334 | 0.327 | NA | NA |
| MGMT | dabrafenib | 0.3282216 | 0.6564431 | 0.32822 | NA | NA |
| IDH2 | docetaxel | 0.3288933 | 0.7454914 | 0.329 | NA | NA |
| TSC2 | lapatinib | 0.3311360 | 0.8842093 | 0.331 | NA | NA |
| EGFR | midostaurin | 0.3312793 | 0.7508998 | 0.3313 | NA | NA |
| ERBB2 | nilotinib | 0.3322155 | 0.7074000 | 0.332 | NA | NA |
| PDGFB | palbociclib | 0.3327587 | 0.7307299 | 0.3328 | NA | NA |
| ROS1 | nilotinib | 0.3339538 | 0.7074000 | 0.334 | NA | NA |
| ERBB3 | gefitinib | 0.3353927 | 0.8402334 | 0.335 | NA | NA |
| BRAF | imatinib | 0.3365852 | 0.7846892 | 0.337 | NA | NA |
| MET | pazopanib | 0.3375577 | 0.9239682 | 0.3376 | NA | NA |
| ERBB3 | bosutinib monohydrate | 0.3381914 | 0.8678254 | 0.338 | NA | NA |
| RET | vismodegib | 0.3393340 | 0.8104430 | 0.34 | NA | NA |
| ERBB2 | pazopanib | 0.3398016 | 0.9239682 | 0.3398 | NA | NA |
| PDGFRB | rucaparib | 0.3399009 | 0.8376438 | 0.340 | NA | NA |
| MYD88 | rucaparib | 0.3422485 | 0.8376438 | 0.342 | NA | NA |
| PDGFRB | vismodegib | 0.3432087 | 0.8104430 | 0.34 | NA | NA |
| DPYD | rucaparib | 0.3449122 | 0.8376438 | 0.345 | NA | NA |
| DPYD | dasatinib | 0.3450704 | 0.9447103 | 0.345 | NA | NA |
| BRCA1 | alectinib | 0.3475727 | 0.7403839 | 0.348 | NA | NA |
| MET | bosutinib monohydrate | 0.3480988 | 0.8678254 | 0.348 | NA | NA |
| IDH2 | tretinoin | 0.3482943 | 0.5921004 | 0.3483 | NA | NA |
| BRCA2 | belinostat | 0.3501637 | 0.7440979 | 0.350 | NA | NA |
| G6PD | ponatinib | 0.3562978 | 0.9972326 | 0.356 | NA | NA |
| CYP19A1 | alectinib | 0.3564980 | 0.7403839 | 0.356 | NA | NA |
| DNMT3A | vismodegib | 0.3575484 | 0.8104430 | 0.36 | NA | NA |
| PTCH1 | docetaxel | 0.3578141 | 0.7603550 | 0.358 | NA | NA |
| BRAF | nilotinib | 0.3579029 | 0.7074000 | 0.358 | NA | NA |
| KIT | afatinib | 0.3580267 | 0.6762727 | 0.358 | NA | NA |
| MET | sunitinib | 0.3589333 | 0.8777619 | 0.359 | NA | NA |
| BRAF | pazopanib | 0.3592410 | 0.9239682 | 0.3592 | NA | NA |
| PDGFB | gefitinib | 0.3627861 | 0.8402334 | 0.363 | NA | NA |
| BRCA2 | pazopanib | 0.3630866 | 0.9239682 | 0.3631 | NA | NA |
| PDGFRB | lapatinib | 0.3673411 | 0.8842093 | 0.367 | NA | NA |
| TSC1 | lapatinib | 0.3673411 | 0.8842093 | 0.367 | NA | NA |
| TSC1 | pazopanib | 0.3683895 | 0.9239682 | 0.3684 | NA | NA |
| ALK | crizotinib | 0.3700920 | 0.8464147 | 0.370 | NA | NA |
| TSC1 | palbociclib | 0.3704875 | 0.7307299 | 0.3705 | NA | NA |
| NPM1 | crizotinib | 0.3719543 | 0.8464147 | 0.372 | NA | NA |
| G6PD | palbociclib | 0.3728013 | 0.7307299 | 0.3728 | NA | NA |
| ERBB2 | ruxolitinib | 0.3785733 | 0.9526741 | 0.379 | NA | NA |
| PDGFB | dasatinib | 0.3792939 | 0.9447103 | 0.379 | NA | NA |
| KRAS | dasatinib | 0.3806744 | 0.9447103 | 0.381 | NA | NA |
| NPM1 | bosutinib monohydrate | 0.3813570 | 0.8678254 | 0.381 | NA | NA |
| G6PD | nilotinib | 0.3817505 | 0.7074000 | 0.382 | NA | NA |
| DPYD | temozolomide | 0.3822258 | 0.8360585 | 0.3822 | NA | NA |
| ERBB2 | bosutinib monohydrate | 0.3828642 | 0.8678254 | 0.383 | NA | NA |
| PTCH1 | alectinib | 0.3832319 | 0.7403839 | 0.383 | NA | NA |
| BRCA2 | gefitinib | 0.3852457 | 0.8402334 | 0.385 | NA | NA |
| RET | imatinib | 0.3884249 | 0.7846892 | 0.388 | NA | NA |
| ERBB3 | belinostat | 0.3891061 | 0.7587223 | 0.389 | NA | NA |
| BRCA1 | dasatinib | 0.3928660 | 0.9447103 | 0.393 | NA | NA |
| ESR1 | vismodegib | 0.3942862 | 0.8378583 | 0.39 | NA | NA |
| AKT1 | tretinoin | 0.3944562 | 0.6307930 | 0.3945 | NA | NA |
| ALK | dasatinib | 0.3952274 | 0.9447103 | 0.395 | NA | NA |
| TSC1 | alectinib | 0.3956481 | 0.7403839 | 0.396 | NA | NA |
| AKT1 | palbociclib | 0.3961746 | 0.7307299 | 0.3962 | NA | NA |
| CYP19A1 | nilotinib | 0.3966596 | 0.7074000 | 0.397 | NA | NA |
| MET | gefitinib | 0.3977576 | 0.8402334 | 0.398 | NA | NA |
| UGT1A1 | pazopanib | 0.3984406 | 0.9239682 | 0.3984 | NA | NA |
| UGT1A1 | sunitinib | 0.3992388 | 0.8777619 | 0.399 | NA | NA |
| NPM1 | palbociclib | 0.3996308 | 0.7307299 | 0.3996 | NA | NA |
| ALK | temozolomide | 0.4005886 | 0.8360585 | 0.4006 | NA | NA |
| KIT | erlotinib | 0.4010455 | 0.8537089 | 0.401 | NA | NA |
| IDH2 | crizotinib | 0.4011464 | 0.8464147 | 0.401 | NA | NA |
| PDGFRA | rucaparib | 0.4016231 | 0.8467310 | 0.402 | NA | NA |
| UGT1A1 | belinostat | 0.4041103 | 0.7587223 | 0.404 | NA | NA |
| BRCA1 | erlotinib | 0.4046403 | 0.8537089 | 0.405 | NA | NA |
| PDGFB | docetaxel | 0.4060325 | 0.8036630 | 0.406 | NA | NA |
| PML | tretinoin | 0.4081601 | 0.6307930 | 0.4082 | NA | NA |
| DNMT3A | ruxolitinib | 0.4082055 | 0.9526741 | 0.408 | NA | NA |
| PDGFRA | palbociclib | 0.4083491 | 0.7307299 | 0.4083 | NA | NA |
| IDH2 | trametinib | 0.4108540 | 0.7083580 | 0.41085 | NA | NA |
| RET | lapatinib | 0.4130391 | 0.8842093 | 0.413 | NA | NA |
| BRCA1 | trametinib | 0.4159320 | 0.7083580 | 0.41593 | NA | NA |
| DNMT3A | trametinib | 0.4166812 | 0.7083580 | 0.41668 | NA | NA |
| PDGFRA | bosutinib monohydrate | 0.4175132 | 0.8678810 | 0.418 | NA | NA |
| MYD88 | alectinib | 0.4215902 | 0.7403839 | 0.422 | NA | NA |
| BRCA1 | nilotinib | 0.4230452 | 0.7074000 | 0.423 | NA | NA |
| JAK2 | belinostat | 0.4239919 | 0.7587223 | 0.424 | NA | NA |
| ABL1 | dasatinib | 0.4250747 | 0.9447103 | 0.425 | NA | NA |
| ESR1 | docetaxel | 0.4254686 | 0.8036630 | 0.425 | NA | NA |
| ERBB2 | erlotinib | 0.4285389 | 0.8537089 | 0.429 | NA | NA |
| KIT | gefitinib | 0.4300536 | 0.8402334 | 0.430 | NA | NA |
| BRCA1 | ponatinib | 0.4319743 | 0.9972326 | 0.432 | NA | NA |
| UGT1A1 | dasatinib | 0.4335809 | 0.9447103 | 0.434 | NA | NA |
| PDGFB | temozolomide | 0.4372281 | 0.8360585 | 0.4372 | NA | NA |
| DNMT3A | imatinib | 0.4384088 | 0.7846892 | 0.438 | NA | NA |
| FLT3 | temozolomide | 0.4398840 | 0.8360585 | 0.4399 | NA | NA |
| IDH2 | lapatinib | 0.4399819 | 0.8842093 | 0.440 | NA | NA |
| CYP19A1 | midostaurin | 0.4400719 | 0.7825538 | 0.4401 | NA | NA |
| ABL1 | rucaparib | 0.4411690 | 0.8467310 | 0.441 | NA | NA |
| ABL1 | dabrafenib | 0.4415642 | 0.7445082 | 0.44156 | NA | NA |
| KIT | lapatinib | 0.4421047 | 0.8842093 | 0.442 | NA | NA |
| FLT3 | pazopanib | 0.4421181 | 0.9239682 | 0.4421 | NA | NA |
| TSC2 | pazopanib | 0.4425985 | 0.9239682 | 0.4426 | NA | NA |
| MYD88 | nilotinib | 0.4453090 | 0.7074000 | 0.445 | NA | NA |
| ERBB2 | alectinib | 0.4455420 | 0.7403839 | 0.446 | NA | NA |
| ESR1 | crizotinib | 0.4487601 | 0.8464147 | 0.449 | NA | NA |
| AKT1 | dabrafenib | 0.4490980 | 0.7445082 | 0.44910 | NA | NA |
| PDGFRA | dabrafenib | 0.4498286 | 0.7445082 | 0.44983 | NA | NA |
| RET | afatinib | 0.4515995 | 0.7810241 | 0.452 | NA | NA |
| G6PD | tretinoin | 0.4531080 | 0.6698118 | 0.4531 | NA | NA |
| CYP19A1 | dasatinib | 0.4547296 | 0.9447103 | 0.455 | NA | NA |
| PML | bosutinib monohydrate | 0.4556704 | 0.8678810 | 0.456 | NA | NA |
| KRAS | vismodegib | 0.4564329 | 0.8556940 | 0.46 | NA | NA |
| PDGFB | alectinib | 0.4572960 | 0.7403839 | 0.457 | NA | NA |
| CYP19A1 | erlotinib | 0.4583847 | 0.8537089 | 0.458 | NA | NA |
| MYD88 | temozolomide | 0.4590388 | 0.8360585 | 0.4590 | NA | NA |
| EGFR | afatinib | 0.4594260 | 0.7810241 | 0.459 | NA | NA |
| DPYD | bosutinib monohydrate | 0.4594664 | 0.8678810 | 0.459 | NA | NA |
| KIT | temozolomide | 0.4596217 | 0.8360585 | 0.4596 | NA | NA |
| PML | imatinib | 0.4608455 | 0.7846892 | 0.461 | NA | NA |
| JAK2 | nilotinib | 0.4609294 | 0.7074000 | 0.461 | NA | NA |
| DNMT3A | erlotinib | 0.4620527 | 0.8537089 | 0.462 | NA | NA |
| MET | nilotinib | 0.4620552 | 0.7074000 | 0.462 | NA | NA |
| BRCA1 | belinostat | 0.4653768 | 0.7769514 | 0.465 | NA | NA |
| BRAF | erlotinib | 0.4662981 | 0.8537089 | 0.466 | NA | NA |
| PTCH1 | sunitinib | 0.4664159 | 0.8777619 | 0.466 | NA | NA |
| ABL1 | imatinib | 0.4679914 | 0.7846892 | 0.468 | NA | NA |
| BRCA2 | ponatinib | 0.4687534 | 0.9972326 | 0.469 | NA | NA |
| PDGFRB | imatinib | 0.4699331 | 0.7846892 | 0.470 | NA | NA |
| PTCH1 | dasatinib | 0.4723552 | 0.9447103 | 0.472 | NA | NA |
| ERBB3 | palbociclib | 0.4724268 | 0.8031255 | 0.4724 | NA | NA |
| MGMT | trametinib | 0.4735520 | 0.7350776 | 0.47355 | NA | NA |
| TSC2 | vismodegib | 0.4749053 | 0.8556940 | 0.47 | NA | NA |
| PTCH1 | trametinib | 0.4756384 | 0.7350776 | 0.47564 | NA | NA |
| PDGFRB | ruxolitinib | 0.4765472 | 0.9526741 | 0.477 | NA | NA |
| MYD88 | tretinoin | 0.4774785 | 0.6757916 | 0.4775 | NA | NA |
| PDGFRA | vismodegib | 0.4781819 | 0.8556940 | 0.48 | NA | NA |
| BRCA1 | ruxolitinib | 0.4788739 | 0.9526741 | 0.479 | NA | NA |
| G6PD | belinostat | 0.4798818 | 0.7769514 | 0.480 | NA | NA |
| NPM1 | ruxolitinib | 0.4817234 | 0.9526741 | 0.482 | NA | NA |
| PDGFB | ponatinib | 0.4821695 | 0.9972326 | 0.482 | NA | NA |
| G6PD | pazopanib | 0.4835225 | 0.9239682 | 0.4835 | NA | NA |
| ERBB2 | sunitinib | 0.4842706 | 0.8777619 | 0.484 | NA | NA |
| CYP19A1 | docetaxel | 0.4847190 | 0.8413401 | 0.485 | NA | NA |
| PDGFRB | afatinib | 0.4872986 | 0.7852762 | 0.487 | NA | NA |
| KRAS | erlotinib | 0.4886809 | 0.8537089 | 0.489 | NA | NA |
| TSC2 | erlotinib | 0.4915604 | 0.8537089 | 0.492 | NA | NA |
| UGT1A1 | nilotinib | 0.4918297 | 0.7074000 | 0.492 | NA | NA |
| CYP19A1 | lapatinib | 0.4937490 | 0.8940161 | 0.494 | NA | NA |
| PDGFB | dabrafenib | 0.4964153 | 0.7445082 | 0.49642 | NA | NA |
| RET | tretinoin | 0.4969056 | 0.6757916 | 0.4969 | NA | NA |
| ALK | midostaurin | 0.4971993 | 0.7825538 | 0.4972 | NA | NA |
| MYD88 | cabozantinib | 0.4985291 | 0.9262331 | 0.4985 | NA | NA |
| PDGFRA | sunitinib | 0.4989956 | 0.8777619 | 0.499 | NA | NA |
| RET | cabozantinib | 0.4991041 | 0.9262331 | 0.4991 | NA | NA |
| EGFR | nilotinib | 0.4993412 | 0.7074000 | 0.499 | NA | NA |
| ERBB3 | lapatinib | 0.5028840 | 0.8940161 | 0.503 | NA | NA |
| RET | crizotinib | 0.5041789 | 0.8464147 | 0.504 | NA | NA |
| G6PD | imatinib | 0.5046668 | 0.7846892 | 0.505 | NA | NA |
| CYP19A1 | afatinib | 0.5081199 | 0.7852762 | 0.508 | NA | NA |
| DPYD | midostaurin | 0.5086465 | 0.7825538 | 0.5086 | NA | NA |
| ERBB3 | pazopanib | 0.5092517 | 0.9239682 | 0.5093 | NA | NA |
| PDGFRB | sunitinib | 0.5106193 | 0.8777619 | 0.511 | NA | NA |
| BRAF | gefitinib | 0.5109860 | 0.8402334 | 0.511 | NA | NA |
| PML | vismodegib | 0.5118312 | 0.8701130 | 0.51 | NA | NA |
| KIT | palbociclib | 0.5134101 | 0.8071578 | 0.5134 | NA | NA |
| ESR1 | dabrafenib | 0.5138002 | 0.7445082 | 0.51380 | NA | NA |
| PDGFRB | temozolomide | 0.5143244 | 0.8360585 | 0.5143 | NA | NA |
| FLT3 | dabrafenib | 0.5153597 | 0.7445082 | 0.51536 | NA | NA |
| MYD88 | dasatinib | 0.5156798 | 0.9470657 | 0.516 | NA | NA |
| DPYD | ruxolitinib | 0.5165164 | 0.9526741 | 0.517 | NA | NA |
| CYP19A1 | sunitinib | 0.5166344 | 0.8777619 | 0.517 | NA | NA |
| DPYD | docetaxel | 0.5183010 | 0.8413401 | 0.518 | NA | NA |
| MET | docetaxel | 0.5196512 | 0.8413401 | 0.520 | NA | NA |
| DPYD | imatinib | 0.5204070 | 0.7846892 | 0.520 | NA | NA |
| EGFR | imatinib | 0.5206143 | 0.7846892 | 0.521 | NA | NA |
| DPYD | gefitinib | 0.5210093 | 0.8402334 | 0.521 | NA | NA |
| DNMT3A | palbociclib | 0.5222786 | 0.8071578 | 0.5223 | NA | NA |
| DPYD | alectinib | 0.5225472 | 0.8075729 | 0.523 | NA | NA |
| NPM1 | gefitinib | 0.5227495 | 0.8402334 | 0.523 | NA | NA |
| PDGFB | trametinib | 0.5280206 | 0.7805521 | 0.52802 | NA | NA |
| BRAF | sunitinib | 0.5308225 | 0.8777619 | 0.531 | NA | NA |
| MYD88 | midostaurin | 0.5310291 | 0.7825538 | 0.5310 | NA | NA |
| ABL1 | crizotinib | 0.5320626 | 0.8464147 | 0.532 | NA | NA |
| DNMT3A | midostaurin | 0.5328652 | 0.7825538 | 0.5329 | NA | NA |
| G6PD | erlotinib | 0.5348254 | 0.8537089 | 0.535 | NA | NA |
| ERBB3 | nilotinib | 0.5371710 | 0.7305525 | 0.537 | NA | NA |
| TSC2 | imatinib | 0.5394738 | 0.7846892 | 0.539 | NA | NA |
| ABL1 | midostaurin | 0.5402282 | 0.7825538 | 0.5402 | NA | NA |
| PTCH1 | dabrafenib | 0.5410696 | 0.7445082 | 0.54107 | NA | NA |
| BRCA2 | temozolomide | 0.5416844 | 0.8360585 | 0.5417 | NA | NA |
| TSC2 | midostaurin | 0.5433441 | 0.7825538 | 0.5433 | NA | NA |
| AKT1 | cabozantinib | 0.5467795 | 0.9262331 | 0.5468 | NA | NA |
| UGT1A1 | dabrafenib | 0.5474325 | 0.7445082 | 0.54743 | NA | NA |
| PDGFB | midostaurin | 0.5477164 | 0.7825538 | 0.5477 | NA | NA |
| UGT1A1 | temozolomide | 0.5500430 | 0.8360585 | 0.5500 | NA | NA |
| MGMT | crizotinib | 0.5501355 | 0.8464147 | 0.550 | NA | NA |
| RET | bosutinib monohydrate | 0.5509591 | 0.9571596 | 0.551 | NA | NA |
| ROS1 | gefitinib | 0.5511895 | 0.8402334 | 0.551 | NA | NA |
| KIT | midostaurin | 0.5523909 | 0.7825538 | 0.5524 | NA | NA |
| CYP19A1 | pazopanib | 0.5523979 | 0.9239682 | 0.5524 | NA | NA |
| ERBB3 | alectinib | 0.5530430 | 0.8175419 | 0.553 | NA | NA |
| MGMT | ponatinib | 0.5540759 | 0.9972326 | 0.554 | NA | NA |
| AKT1 | belinostat | 0.5547454 | 0.8458949 | 0.555 | NA | NA |
| CYP19A1 | tretinoin | 0.5549899 | 0.7257560 | 0.5550 | NA | NA |
| TSC2 | dasatinib | 0.5568736 | 0.9470657 | 0.557 | NA | NA |
| MYD88 | erlotinib | 0.5580136 | 0.8537089 | 0.558 | NA | NA |
| ALK | pazopanib | 0.5581192 | 0.9239682 | 0.5581 | NA | NA |
| RET | ruxolitinib | 0.5597886 | 0.9526741 | 0.560 | NA | NA |
| ERBB3 | afatinib | 0.5614904 | 0.7959129 | 0.561 | NA | NA |
| JAK2 | crizotinib | 0.5623793 | 0.8464147 | 0.562 | NA | NA |
| PML | pazopanib | 0.5629739 | 0.9239682 | 0.5630 | NA | NA |
| TSC1 | erlotinib | 0.5633547 | 0.8537089 | 0.563 | NA | NA |
| ESR1 | sunitinib | 0.5643768 | 0.8777619 | 0.564 | NA | NA |
| G6PD | rucaparib | 0.5646292 | 0.8467310 | 0.565 | NA | NA |
| RET | gefitinib | 0.5658382 | 0.8402334 | 0.566 | NA | NA |
| PDGFB | sunitinib | 0.5660424 | 0.8777619 | 0.566 | NA | NA |
| FLT3 | sunitinib | 0.5660424 | 0.8777619 | 0.566 | NA | NA |
| EGFR | temozolomide | 0.5669345 | 0.8360585 | 0.5669 | NA | NA |
| JAK2 | palbociclib | 0.5675682 | 0.8390139 | 0.5676 | NA | NA |
| FLT3 | lapatinib | 0.5679419 | 0.9537394 | 0.568 | NA | NA |
| CYP19A1 | gefitinib | 0.5683932 | 0.8402334 | 0.568 | NA | NA |
| JAK2 | erlotinib | 0.5702807 | 0.8537089 | 0.570 | NA | NA |
| TSC2 | cabozantinib | 0.5710996 | 0.9262331 | 0.5711 | NA | NA |
| TSC1 | docetaxel | 0.5725527 | 0.8563752 | 0.573 | NA | NA |
| BRCA1 | rucaparib | 0.5768966 | 0.8467310 | 0.577 | NA | NA |
| MGMT | belinostat | 0.5789471 | 0.8458949 | 0.579 | NA | NA |
| ALK | cabozantinib | 0.5795396 | 0.9262331 | 0.5795 | NA | NA |
| ABL1 | sunitinib | 0.5802023 | 0.8777619 | 0.580 | NA | NA |
| ROS1 | midostaurin | 0.5814725 | 0.7908026 | 0.5815 | NA | NA |
| ALK | rucaparib | 0.5819295 | 0.8467310 | 0.582 | NA | NA |
| TSC2 | ruxolitinib | 0.5824296 | 0.9526741 | 0.582 | NA | NA |
| PDGFRA | docetaxel | 0.5828922 | 0.8563752 | 0.583 | NA | NA |
| PTCH1 | ruxolitinib | 0.5835921 | 0.9526741 | 0.584 | NA | NA |
| RET | ponatinib | 0.5838741 | 0.9972326 | 0.584 | NA | NA |
| RET | nilotinib | 0.5840052 | 0.7528214 | 0.584 | NA | NA |
| TSC2 | rucaparib | 0.5851976 | 0.8467310 | 0.585 | NA | NA |
| NPM1 | ponatinib | 0.5854791 | 0.9972326 | 0.585 | NA | NA |
| BRCA1 | afatinib | 0.5859699 | 0.7959129 | 0.586 | NA | NA |
| EGFR | ponatinib | 0.5861711 | 0.9972326 | 0.586 | NA | NA |
| PDGFRA | temozolomide | 0.5883211 | 0.8360585 | 0.5883 | NA | NA |
| EGFR | tretinoin | 0.5940328 | 0.7480413 | 0.5940 | NA | NA |
| KIT | pazopanib | 0.5948891 | 0.9239682 | 0.5949 | NA | NA |
| PML | rucaparib | 0.5950165 | 0.8467310 | 0.595 | NA | NA |
| EGFR | lapatinib | 0.5960871 | 0.9537394 | 0.596 | NA | NA |
| ESR1 | ruxolitinib | 0.5973766 | 0.9526741 | 0.597 | NA | NA |
| MGMT | nilotinib | 0.5978288 | 0.7528214 | 0.598 | NA | NA |
| MYD88 | vismodegib | 0.5979041 | 0.9680352 | 0.60 | NA | NA |
| ABL1 | erlotinib | 0.5985108 | 0.8537089 | 0.599 | NA | NA |
| IDH2 | sunitinib | 0.6010327 | 0.8777619 | 0.601 | NA | NA |
| CYP19A1 | cabozantinib | 0.6024929 | 0.9262331 | 0.6025 | NA | NA |
| BRAF | crizotinib | 0.6026642 | 0.8464147 | 0.603 | NA | NA |
| TPMT | trametinib | 0.6050220 | 0.8571145 | 0.60502 | NA | NA |
| ROS1 | sunitinib | 0.6060667 | 0.8777619 | 0.606 | NA | NA |
| BRCA2 | docetaxel | 0.6116514 | 0.8563752 | 0.612 | NA | NA |
| TSC1 | ponatinib | 0.6125905 | 0.9972326 | 0.613 | NA | NA |
| MET | ponatinib | 0.6159349 | 0.9972326 | 0.616 | NA | NA |
| PML | ponatinib | 0.6178115 | 0.9972326 | 0.618 | NA | NA |
| AKT1 | pazopanib | 0.6189835 | 0.9239682 | 0.6190 | NA | NA |
| CYP19A1 | crizotinib | 0.6190452 | 0.8464147 | 0.619 | NA | NA |
| JAK2 | afatinib | 0.6195384 | 0.7959129 | 0.620 | NA | NA |
| G6PD | sunitinib | 0.6213525 | 0.8777619 | 0.621 | NA | NA |
| MGMT | bosutinib monohydrate | 0.6222029 | 0.9571596 | 0.622 | NA | NA |
| KRAS | gefitinib | 0.6235545 | 0.8503583 | 0.624 | NA | NA |
| DNMT3A | tretinoin | 0.6240726 | 0.7578025 | 0.6241 | NA | NA |
| PDGFB | belinostat | 0.6267736 | 0.8458949 | 0.627 | NA | NA |
| MYD88 | pazopanib | 0.6271722 | 0.9239682 | 0.6272 | NA | NA |
| ROS1 | afatinib | 0.6282804 | 0.7959129 | 0.628 | NA | NA |
| TPMT | afatinib | 0.6320485 | 0.7959129 | 0.632 | NA | NA |
| AKT1 | trametinib | 0.6346674 | 0.8631476 | 0.63467 | NA | NA |
| EGFR | sunitinib | 0.6347395 | 0.8777619 | 0.635 | NA | NA |
| PML | erlotinib | 0.6360548 | 0.8537089 | 0.636 | NA | NA |
| PDGFRB | alectinib | 0.6381495 | 0.8897754 | 0.638 | NA | NA |
| KRAS | imatinib | 0.6424818 | 0.8938878 | 0.642 | NA | NA |
| MGMT | sunitinib | 0.6441449 | 0.8777619 | 0.644 | NA | NA |
| EGFR | ruxolitinib | 0.6447588 | 0.9526741 | 0.645 | NA | NA |
| NPM1 | rucaparib | 0.6448258 | 0.8467310 | 0.645 | NA | NA |
| DNMT3A | ponatinib | 0.6448404 | 0.9972326 | 0.645 | NA | NA |
| KRAS | lapatinib | 0.6456344 | 0.9838238 | 0.646 | NA | NA |
| UGT1A1 | gefitinib | 0.6466857 | 0.8503583 | 0.647 | NA | NA |
| PDGFB | rucaparib | 0.6469333 | 0.8467310 | 0.647 | NA | NA |
| ALK | docetaxel | 0.6482988 | 0.8563752 | 0.648 | NA | NA |
| FLT3 | midostaurin | 0.6526579 | 0.8534757 | 0.6527 | NA | NA |
| ERBB3 | ruxolitinib | 0.6532068 | 0.9526741 | 0.653 | NA | NA |
| TSC2 | gefitinib | 0.6534622 | 0.8503583 | 0.653 | NA | NA |
| UGT1A1 | alectinib | 0.6542466 | 0.8897754 | 0.654 | NA | NA |
| TSC2 | bosutinib monohydrate | 0.6543872 | 0.9571596 | 0.654 | NA | NA |
| KIT | sunitinib | 0.6583214 | 0.8777619 | 0.658 | NA | NA |
| PTCH1 | crizotinib | 0.6605698 | 0.8464147 | 0.661 | NA | NA |
| PDGFRB | pazopanib | 0.6626651 | 0.9239682 | 0.6627 | NA | NA |
| IDH2 | erlotinib | 0.6634451 | 0.8537089 | 0.663 | NA | NA |
| MGMT | temozolomide | 0.6634570 | 0.8360585 | 0.6635 | NA | NA |
| ALK | vismodegib | 0.6657344 | 0.9773105 | 0.67 | NA | NA |
| MYD88 | palbociclib | 0.6675616 | 0.8695381 | 0.6676 | NA | NA |
| FLT3 | belinostat | 0.6686147 | 0.8458949 | 0.669 | NA | NA |
| FLT3 | ponatinib | 0.6691061 | 0.9972326 | 0.669 | NA | NA |
| PDGFB | crizotinib | 0.6714054 | 0.8464147 | 0.671 | NA | NA |
| DNMT3A | dabrafenib | 0.6722330 | 0.8621835 | 0.67223 | NA | NA |
| FLT3 | docetaxel | 0.6723654 | 0.8563752 | 0.672 | NA | NA |
| MET | ruxolitinib | 0.6724758 | 0.9526741 | 0.672 | NA | NA |
| ROS1 | pazopanib | 0.6730661 | 0.9239682 | 0.6731 | NA | NA |
| BRCA2 | nilotinib | 0.6739857 | 0.8184112 | 0.674 | NA | NA |
| ROS1 | temozolomide | 0.6751390 | 0.8360585 | 0.6751 | NA | NA |
| PML | gefitinib | 0.6752846 | 0.8503583 | 0.675 | NA | NA |
| AKT1 | rucaparib | 0.6766724 | 0.8467310 | 0.677 | NA | NA |
| EGFR | belinostat | 0.6783585 | 0.8458949 | 0.678 | NA | NA |
| ESR1 | dasatinib | 0.6806688 | 0.9470657 | 0.681 | NA | NA |
| ERBB2 | rucaparib | 0.6813788 | 0.8467310 | 0.681 | NA | NA |
| ESR1 | lapatinib | 0.6823352 | 0.9878187 | 0.682 | NA | NA |
| PDGFRA | erlotinib | 0.6824019 | 0.8537089 | 0.682 | NA | NA |
| PDGFRA | ponatinib | 0.6831311 | 0.9972326 | 0.683 | NA | NA |
| ESR1 | midostaurin | 0.6835330 | 0.8607452 | 0.6835 | NA | NA |
| ESR1 | tretinoin | 0.6845216 | 0.8025426 | 0.6845 | NA | NA |
| BRCA1 | dabrafenib | 0.6846752 | 0.8621835 | 0.68468 | NA | NA |
| KRAS | rucaparib | 0.6847697 | 0.8467310 | 0.685 | NA | NA |
| BRCA1 | palbociclib | 0.6850052 | 0.8695381 | 0.6850 | NA | NA |
| RET | belinostat | 0.6890334 | 0.8458949 | 0.689 | NA | NA |
| MYD88 | crizotinib | 0.6896981 | 0.8464147 | 0.690 | NA | NA |
| CYP19A1 | bosutinib monohydrate | 0.6902719 | 0.9571596 | 0.690 | NA | NA |
| MGMT | pazopanib | 0.6911734 | 0.9239682 | 0.6912 | NA | NA |
| ALK | alectinib | 0.6916060 | 0.9044078 | 0.692 | NA | NA |
| MET | temozolomide | 0.6917583 | 0.8360585 | 0.6918 | NA | NA |
| ESR1 | pazopanib | 0.6922709 | 0.9239682 | 0.6923 | NA | NA |
| PML | cabozantinib | 0.6926459 | 0.9262331 | 0.6926 | NA | NA |
| PDGFB | cabozantinib | 0.6931930 | 0.9262331 | 0.6932 | NA | NA |
| ESR1 | trametinib | 0.6962680 | 0.9060078 | 0.69627 | NA | NA |
| ABL1 | temozolomide | 0.6987934 | 0.8360585 | 0.6988 | NA | NA |
| BRCA1 | docetaxel | 0.7001716 | 0.8563752 | 0.700 | NA | NA |
| BRCA1 | crizotinib | 0.7017863 | 0.8464147 | 0.702 | NA | NA |
| PML | dasatinib | 0.7028188 | 0.9470657 | 0.703 | NA | NA |
| TSC1 | dasatinib | 0.7033301 | 0.9470657 | 0.703 | NA | NA |
| G6PD | crizotinib | 0.7040235 | 0.8464147 | 0.704 | NA | NA |
| ERBB2 | docetaxel | 0.7052502 | 0.8563752 | 0.705 | NA | NA |
| UGT1A1 | ponatinib | 0.7062488 | 0.9972326 | 0.706 | NA | NA |
| ROS1 | vismodegib | 0.7075936 | 0.9773105 | 0.71 | NA | NA |
| ERBB2 | palbociclib | 0.7083268 | 0.8695381 | 0.7083 | NA | NA |
| TSC2 | belinostat | 0.7089749 | 0.8458949 | 0.709 | NA | NA |
| IDH2 | dasatinib | 0.7090830 | 0.9470657 | 0.709 | NA | NA |
| ALK | erlotinib | 0.7099827 | 0.8537089 | 0.710 | NA | NA |
| JAK2 | dasatinib | 0.7103203 | 0.9470657 | 0.710 | NA | NA |
| RET | dabrafenib | 0.7105653 | 0.8628293 | 0.71057 | NA | NA |
| KRAS | ruxolitinib | 0.7137147 | 0.9613264 | 0.714 | NA | NA |
| RET | dasatinib | 0.7148163 | 0.9470657 | 0.715 | NA | NA |
| KRAS | temozolomide | 0.7150718 | 0.8360585 | 0.7151 | NA | NA |
| ESR1 | cabozantinib | 0.7161231 | 0.9262331 | 0.7161 | NA | NA |
| EGFR | trametinib | 0.7194767 | 0.9060078 | 0.71948 | NA | NA |
| PTCH1 | vismodegib | 0.7198241 | 0.9773105 | 0.72 | NA | NA |
| ERBB3 | erlotinib | 0.7203169 | 0.8537089 | 0.720 | NA | NA |
| PDGFRB | ponatinib | 0.7240517 | 0.9972326 | 0.724 | NA | NA |
| ERBB3 | rucaparib | 0.7263040 | 0.8467310 | 0.726 | NA | NA |
| DPYD | pazopanib | 0.7284979 | 0.9239682 | 0.7285 | NA | NA |
| PDGFRB | palbociclib | 0.7303977 | 0.8695381 | 0.7304 | NA | NA |
| ABL1 | nilotinib | 0.7313136 | 0.8564973 | 0.731 | NA | NA |
| BRAF | temozolomide | 0.7335771 | 0.8360585 | 0.7336 | NA | NA |
| EGFR | docetaxel | 0.7346881 | 0.8613585 | 0.735 | NA | NA |
| PML | ruxolitinib | 0.7351319 | 0.9613264 | 0.735 | NA | NA |
| CYP19A1 | temozolomide | 0.7376987 | 0.8360585 | 0.7377 | NA | NA |
| PDGFRA | crizotinib | 0.7390621 | 0.8464147 | 0.739 | NA | NA |
| KIT | dasatinib | 0.7398951 | 0.9470657 | 0.740 | NA | NA |
| ERBB3 | crizotinib | 0.7406129 | 0.8464147 | 0.741 | NA | NA |
| AKT1 | afatinib | 0.7407741 | 0.8995114 | 0.741 | NA | NA |
| DPYD | sunitinib | 0.7414533 | 0.8823886 | 0.741 | NA | NA |
| KRAS | bosutinib monohydrate | 0.7414809 | 0.9571596 | 0.741 | NA | NA |
| TSC1 | cabozantinib | 0.7417760 | 0.9262331 | 0.7418 | NA | NA |
| CYP19A1 | ponatinib | 0.7421820 | 0.9972326 | 0.742 | NA | NA |
| PDGFRB | bosutinib monohydrate | 0.7429860 | 0.9571596 | 0.743 | NA | NA |
| IDH2 | imatinib | 0.7435570 | 0.9237192 | 0.744 | NA | NA |
| PDGFRA | belinostat | 0.7450686 | 0.8458949 | 0.745 | NA | NA |
| TPMT | midostaurin | 0.7460273 | 0.9058903 | 0.7460 | NA | NA |
| PML | belinostat | 0.7463779 | 0.8458949 | 0.746 | NA | NA |
| BRCA1 | imatinib | 0.7500850 | 0.9237192 | 0.750 | NA | NA |
| KIT | imatinib | 0.7505218 | 0.9237192 | 0.751 | NA | NA |
| EGFR | palbociclib | 0.7514260 | 0.8695381 | 0.7514 | NA | NA |
| DNMT3A | bosutinib monohydrate | 0.7551741 | 0.9571596 | 0.755 | NA | NA |
| PDGFRA | pazopanib | 0.7583124 | 0.9239682 | 0.7583 | NA | NA |
| DNMT3A | alectinib | 0.7613631 | 0.9273034 | 0.761 | NA | NA |
| TPMT | rucaparib | 0.7619662 | 0.8467310 | 0.762 | NA | NA |
| AKT1 | gefitinib | 0.7625117 | 0.8968173 | 0.763 | NA | NA |
| G6PD | trametinib | 0.7631155 | 0.9266403 | 0.76312 | NA | NA |
| EGFR | pazopanib | 0.7631271 | 0.9239682 | 0.7631 | NA | NA |
| MGMT | alectinib | 0.7636616 | 0.9273034 | 0.764 | NA | NA |
| PDGFB | bosutinib monohydrate | 0.7637526 | 0.9571596 | 0.764 | NA | NA |
| KRAS | sunitinib | 0.7642647 | 0.8823886 | 0.764 | NA | NA |
| PDGFRB | gefitinib | 0.7649324 | 0.8968173 | 0.765 | NA | NA |
| TPMT | palbociclib | 0.7668585 | 0.8695381 | 0.7669 | NA | NA |
| CYP19A1 | palbociclib | 0.7672395 | 0.8695381 | 0.7672 | NA | NA |
| ABL1 | bosutinib monohydrate | 0.7708229 | 0.9571596 | 0.771 | NA | NA |
| ALK | tretinoin | 0.7717427 | 0.8561605 | 0.7717 | NA | NA |
| PDGFRA | lapatinib | 0.7718304 | 0.9878187 | 0.772 | NA | NA |
| PDGFB | pazopanib | 0.7722360 | 0.9239682 | 0.7722 | NA | NA |
| ERBB2 | vismodegib | 0.7739594 | 0.9773105 | 0.77 | NA | NA |
| KIT | docetaxel | 0.7747007 | 0.8752363 | 0.775 | NA | NA |
| PML | nilotinib | 0.7777017 | 0.8564973 | 0.778 | NA | NA |
| DPYD | tretinoin | 0.7806169 | 0.8561605 | 0.7806 | NA | NA |
| EGFR | rucaparib | 0.7812134 | 0.8467310 | 0.781 | NA | NA |
| MET | rucaparib | 0.7852325 | 0.8467310 | 0.785 | NA | NA |
| MYD88 | sunitinib | 0.7863908 | 0.8823886 | 0.786 | NA | NA |
| NPM1 | pazopanib | 0.7880905 | 0.9239682 | 0.7881 | NA | NA |
| MYD88 | imatinib | 0.7889569 | 0.9350600 | 0.789 | NA | NA |
| BRAF | ponatinib | 0.7903167 | 0.9972326 | 0.790 | NA | NA |
| BRCA1 | gefitinib | 0.7929047 | 0.8986254 | 0.793 | NA | NA |
| FLT3 | alectinib | 0.7941809 | 0.9311087 | 0.794 | NA | NA |
| BRAF | midostaurin | 0.7943467 | 0.9164533 | 0.7943 | NA | NA |
| PTCH1 | rucaparib | 0.7952280 | 0.8467310 | 0.795 | NA | NA |
| PML | docetaxel | 0.7980096 | 0.8752363 | 0.798 | NA | NA |
| NPM1 | vismodegib | 0.8004491 | 0.9773105 | 0.80 | NA | NA |
| PDGFRB | crizotinib | 0.8019048 | 0.8848604 | 0.802 | NA | NA |
| ERBB3 | trametinib | 0.8021031 | 0.9403967 | 0.80210 | NA | NA |
| FLT3 | afatinib | 0.8043606 | 0.9430434 | 0.804 | NA | NA |
| JAK2 | sunitinib | 0.8046870 | 0.8823886 | 0.805 | NA | NA |
| KRAS | nilotinib | 0.8058237 | 0.8564973 | 0.806 | NA | NA |
| IDH2 | nilotinib | 0.8061151 | 0.8564973 | 0.806 | NA | NA |
| IDH2 | ruxolitinib | 0.8073056 | 0.9802461 | 0.807 | NA | NA |
| FLT3 | tretinoin | 0.8076478 | 0.8581257 | 0.8076 | NA | NA |
| DPYD | belinostat | 0.8079628 | 0.8861528 | 0.808 | NA | NA |
| ESR1 | bosutinib monohydrate | 0.8080005 | 0.9571596 | 0.808 | NA | NA |
| DPYD | palbociclib | 0.8111267 | 0.8753990 | 0.8111 | NA | NA |
| RET | temozolomide | 0.8158960 | 0.8948536 | 0.8159 | NA | NA |
| BRCA1 | sunitinib | 0.8165800 | 0.8823886 | 0.817 | NA | NA |
| ERBB3 | dasatinib | 0.8180600 | 0.9608776 | 0.818 | NA | NA |
| G6PD | gefitinib | 0.8202116 | 0.8995869 | 0.820 | NA | NA |
| FLT3 | palbociclib | 0.8239049 | 0.8753990 | 0.8239 | NA | NA |
| EGFR | bosutinib monohydrate | 0.8249647 | 0.9571596 | 0.825 | NA | NA |
| BRCA1 | pazopanib | 0.8251732 | 0.9335674 | 0.8252 | NA | NA |
| MET | alectinib | 0.8262519 | 0.9364188 | 0.826 | NA | NA |
| G6PD | cabozantinib | 0.8264953 | 0.9262331 | 0.8265 | NA | NA |
| ERBB3 | sunitinib | 0.8272393 | 0.8823886 | 0.827 | NA | NA |
| TSC1 | dabrafenib | 0.8273766 | 0.9700277 | 0.82738 | NA | NA |
| G6PD | midostaurin | 0.8281741 | 0.9164533 | 0.8282 | NA | NA |
| FLT3 | ruxolitinib | 0.8312495 | 0.9802461 | 0.831 | NA | NA |
| MET | trametinib | 0.8326323 | 0.9436500 | 0.83263 | NA | NA |
| BRCA1 | cabozantinib | 0.8333837 | 0.9262331 | 0.8334 | NA | NA |
| MGMT | tretinoin | 0.8349168 | 0.8602173 | 0.8349 | NA | NA |
| CYP19A1 | rucaparib | 0.8350834 | 0.8467310 | 0.835 | NA | NA |
| MET | midostaurin | 0.8355898 | 0.9164533 | 0.8356 | NA | NA |
| RET | rucaparib | 0.8423514 | 0.8467310 | 0.842 | NA | NA |
| BRAF | cabozantinib | 0.8425783 | 0.9262331 | 0.8426 | NA | NA |
| UGT1A1 | rucaparib | 0.8467310 | 0.8467310 | 0.847 | NA | NA |
| ERBB2 | cabozantinib | 0.8477762 | 0.9262331 | 0.8478 | NA | NA |
| DNMT3A | gefitinib | 0.8493836 | 0.9024701 | 0.849 | NA | NA |
| TPMT | pazopanib | 0.8511938 | 0.9335674 | 0.8512 | NA | NA |
| KRAS | crizotinib | 0.8512775 | 0.8966708 | 0.851 | NA | NA |
| MET | cabozantinib | 0.8512783 | 0.9262331 | 0.8513 | NA | NA |
| JAK2 | imatinib | 0.8521878 | 0.9739289 | 0.852 | NA | NA |
| JAK2 | ruxolitinib | 0.8523436 | 0.9802461 | 0.852 | NA | NA |
| UGT1A1 | docetaxel | 0.8542969 | 0.9076904 | 0.854 | NA | NA |
| MET | dasatinib | 0.8543593 | 0.9608776 | 0.854 | NA | NA |
| MYD88 | ponatinib | 0.8552763 | 0.9972326 | 0.855 | NA | NA |
| DPYD | erlotinib | 0.8604995 | 0.9307227 | 0.860 | NA | NA |
| ROS1 | palbociclib | 0.8627523 | 0.8888963 | 0.8628 | NA | NA |
| NPM1 | afatinib | 0.8655570 | 0.9518372 | 0.866 | NA | NA |
| UGT1A1 | vismodegib | 0.8657073 | 0.9773105 | 0.87 | NA | NA |
| NPM1 | trametinib | 0.8672776 | 0.9512077 | 0.86728 | NA | NA |
| G6PD | dasatinib | 0.8682306 | 0.9608776 | 0.868 | NA | NA |
| KIT | crizotinib | 0.8686498 | 0.8966708 | 0.869 | NA | NA |
| ESR1 | ponatinib | 0.8695576 | 0.9972326 | 0.870 | NA | NA |
| FLT3 | bosutinib monohydrate | 0.8695733 | 0.9571596 | 0.870 | NA | NA |
| DNMT3A | lapatinib | 0.8744953 | 0.9878187 | 0.874 | NA | NA |
| ERBB3 | vismodegib | 0.8804120 | 0.9773105 | 0.88 | NA | NA |
| TPMT | ponatinib | 0.8811769 | 0.9972326 | 0.881 | NA | NA |
| JAK2 | midostaurin | 0.8847197 | 0.9400146 | 0.8847 | NA | NA |
| BRCA2 | ruxolitinib | 0.8869414 | 0.9802461 | 0.887 | NA | NA |
| MYD88 | bosutinib monohydrate | 0.8892270 | 0.9571596 | 0.889 | NA | NA |
| JAK2 | pazopanib | 0.8907594 | 0.9464319 | 0.8908 | NA | NA |
| BRCA2 | cabozantinib | 0.8957636 | 0.9262331 | 0.8958 | NA | NA |
| ROS1 | ruxolitinib | 0.8966205 | 0.9802461 | 0.897 | NA | NA |
| PML | trametinib | 0.8969530 | 0.9530125 | 0.89695 | NA | NA |
| MGMT | dasatinib | 0.8989855 | 0.9608776 | 0.899 | NA | NA |
| ALK | bosutinib monohydrate | 0.9008561 | 0.9571596 | 0.901 | NA | NA |
| BRAF | afatinib | 0.9011510 | 0.9518372 | 0.901 | NA | NA |
| ROS1 | crizotinib | 0.9055984 | 0.9055984 | 0.906 | NA | NA |
| TSC1 | belinostat | 0.9061702 | 0.9585223 | 0.906 | NA | NA |
| ERBB3 | docetaxel | 0.9076995 | 0.9352056 | 0.908 | NA | NA |
| AKT1 | temozolomide | 0.9094399 | 0.9462406 | 0.9094 | NA | NA |
| CYP19A1 | dabrafenib | 0.9107211 | 0.9949724 | 0.91072 | NA | NA |
| ESR1 | erlotinib | 0.9133687 | 0.9307227 | 0.913 | NA | NA |
| BRCA1 | lapatinib | 0.9142372 | 0.9878187 | 0.914 | NA | NA |
| EGFR | cabozantinib | 0.9149328 | 0.9262331 | 0.9149 | NA | NA |
| BRCA2 | sunitinib | 0.9151190 | 0.9216497 | 0.915 | NA | NA |
| TSC1 | gefitinib | 0.9156569 | 0.9283678 | 0.916 | NA | NA |
| ROS1 | imatinib | 0.9157097 | 1.0000000 | 0.916 | NA | NA |
| ERBB2 | ponatinib | 0.9158815 | 0.9972326 | 0.916 | NA | NA |
| BRAF | dasatinib | 0.9161548 | 0.9608776 | 0.916 | NA | NA |
| BRCA2 | dabrafenib | 0.9168207 | 0.9949724 | 0.91682 | NA | NA |
| G6PD | temozolomide | 0.9184100 | 0.9462406 | 0.9184 | NA | NA |
| JAK2 | lapatinib | 0.9210478 | 0.9878187 | 0.921 | NA | NA |
| NPM1 | sunitinib | 0.9216497 | 0.9216497 | 0.922 | NA | NA |
| EGFR | erlotinib | 0.9218958 | 0.9307227 | 0.922 | NA | NA |
| ROS1 | lapatinib | 0.9246091 | 0.9878187 | 0.925 | NA | NA |
| PDGFRA | ruxolitinib | 0.9248089 | 0.9802461 | 0.925 | NA | NA |
| KIT | ponatinib | 0.9257639 | 0.9972326 | 0.926 | NA | NA |
| UGT1A1 | cabozantinib | 0.9262331 | 0.9262331 | 0.9262 | NA | NA |
| PTCH1 | erlotinib | 0.9275623 | 0.9307227 | 0.928 | NA | NA |
| MYD88 | gefitinib | 0.9283678 | 0.9283678 | 0.928 | NA | NA |
| TSC1 | afatinib | 0.9300086 | 0.9518372 | 0.930 | NA | NA |
| KIT | belinostat | 0.9303304 | 0.9585223 | 0.930 | NA | NA |
| RET | erlotinib | 0.9307227 | 0.9307227 | 0.931 | NA | NA |
| MYD88 | lapatinib | 0.9323054 | 0.9878187 | 0.932 | NA | NA |
| MGMT | vismodegib | 0.9400649 | 0.9773105 | 0.94 | NA | NA |
| BRCA2 | trametinib | 0.9421624 | 0.9707128 | 0.94216 | NA | NA |
| IDH2 | alectinib | 0.9437117 | 0.9851623 | 0.944 | NA | NA |
| IDH2 | palbociclib | 0.9443484 | 0.9443484 | 0.9443 | NA | NA |
| EGFR | vismodegib | 0.9448114 | 0.9773105 | 0.94 | NA | NA |
| IDH2 | midostaurin | 0.9477169 | 0.9563247 | 0.9477 | NA | NA |
| ABL1 | vismodegib | 0.9494533 | 0.9773105 | 0.95 | NA | NA |
| ESR1 | afatinib | 0.9503087 | 0.9518372 | 0.950 | NA | NA |
| ROS1 | dasatinib | 0.9512458 | 0.9608776 | 0.951 | NA | NA |
| UGT1A1 | ruxolitinib | 0.9514154 | 0.9802461 | 0.951 | NA | NA |
| PML | afatinib | 0.9518372 | 0.9518372 | 0.952 | NA | NA |
| BRCA1 | temozolomide | 0.9526259 | 0.9526259 | 0.9526 | NA | NA |
| ALK | ponatinib | 0.9561548 | 0.9972326 | 0.956 | NA | NA |
| RET | midostaurin | 0.9563247 | 0.9563247 | 0.9563 | NA | NA |
| BRAF | lapatinib | 0.9579143 | 0.9878187 | 0.958 | NA | NA |
| RET | pazopanib | 0.9581510 | 0.9871859 | 0.9582 | NA | NA |
| PDGFRA | dasatinib | 0.9608776 | 0.9608776 | 0.961 | NA | NA |
| ALK | imatinib | 0.9639389 | 1.0000000 | 0.964 | NA | NA |
| DPYD | nilotinib | 0.9678380 | 0.9911966 | 0.968 | NA | NA |
| G6PD | lapatinib | 0.9681165 | 0.9878187 | 0.968 | NA | NA |
| IDH2 | dabrafenib | 0.9684328 | 0.9949724 | 0.96843 | NA | NA |
| KIT | alectinib | 0.9692528 | 0.9851623 | 0.969 | NA | NA |
| AKT1 | docetaxel | 0.9695144 | 0.9695144 | 0.970 | NA | NA |
| DNMT3A | belinostat | 0.9723117 | 0.9723117 | 0.972 | NA | NA |
| CYP19A1 | vismodegib | 0.9723531 | 0.9773105 | 0.97 | NA | NA |
| BRCA2 | vismodegib | 0.9733078 | 0.9773105 | 0.97 | NA | NA |
| PML | lapatinib | 0.9738117 | 0.9878187 | 0.974 | NA | NA |
| FLT3 | vismodegib | 0.9773105 | 0.9773105 | 0.98 | NA | NA |
| MYD88 | dabrafenib | 0.9773916 | 0.9949724 | 0.97739 | NA | NA |
| PDGFRB | trametinib | 0.9784811 | 0.9784811 | 0.97848 | NA | NA |
| KRAS | alectinib | 0.9838427 | 0.9851623 | 0.984 | NA | NA |
| TPMT | bosutinib monohydrate | 0.9847665 | 0.9984574 | 0.985 | NA | NA |
| ESR1 | alectinib | 0.9851623 | 0.9851623 | 0.985 | NA | NA |
| PTCH1 | lapatinib | 0.9878187 | 0.9878187 | 0.988 | NA | NA |
| PTCH1 | imatinib | 0.9882665 | 1.0000000 | 0.988 | NA | NA |
| JAK2 | ponatinib | 0.9882767 | 0.9972326 | 0.988 | NA | NA |
| ALK | nilotinib | 0.9911966 | 0.9911966 | 0.991 | NA | NA |
| MGMT | ruxolitinib | 0.9946721 | 0.9946721 | 0.995 | NA | NA |
| ROS1 | dabrafenib | 0.9949724 | 0.9949724 | 0.99497 | NA | NA |
| ABL1 | tretinoin | 0.9968006 | 0.9968006 | 0.9968 | NA | NA |
| AKT1 | ponatinib | 0.9972326 | 0.9972326 | 0.997 | NA | NA |
| JAK2 | bosutinib monohydrate | 0.9984574 | 0.9984574 | 0.998 | NA | NA |
| DNMT3A | pazopanib | 0.9995159 | 0.9995159 | 0.9995 | NA | NA |
| MGMT | imatinib | 1.0000000 | 1.0000000 | 1.000 | NA | NA |
Mutation status boxplots for genes identified in G2P.
Boxplots ordered by gene based on frequency of G2P associations.
crispr_data_g2p$Hugo_Symbol <- factor(crispr_data_g2p$Hugo_Symbol, levels = g2p_genes)
crispr_data_g2p_color <- as.character(crispr_data_g2p$Color_Nonsilent)
names(crispr_data_g2p_color) <- crispr_data_g2p$Mutation_Status_Nonsilent
crispr_label_text <- data.frame(p.signif.adj = crispr_signif_g2p_gene$p.signif.adj, p.signif = crispr_signif_g2p_gene$p.signif, Hugo_Symbol = crispr_signif_g2p_gene$Hugo_Symbol)
crispr_label_text <- filter(crispr_label_text, Hugo_Symbol %in% g2p_genes)
crispr_label_text$Hugo_Symbol <- factor(crispr_label_text$Hugo_Symbol, levels = g2p_genes)
crispr_data_g2p_plot <- ggplot(data = crispr_data_g2p, aes(x = Mutation_Status_Nonsilent, y = Score)) +
facet_wrap(~ Hugo_Symbol, drop = FALSE, nrow = 1) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(mapping = aes(fill = Mutation_Status_Nonsilent), position = position_dodge(0.85)) +
scale_fill_manual(values = crispr_data_g2p_color) +
guides(color = FALSE) +
geom_text(data = crispr_label_text, mapping = aes(x = 1.5, y = 2, label = p.signif), nudge_y = 0.1) +
theme(legend.position = "top", axis.ticks.x = element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank()) +
labs(title = "CRISPR", fill = "Mutation Status", y = "CERES Score", x = "Mutation Status")
crispr_data_g2p_plot
# ggsave("./plots_18Q3/manuscript/crispr_data_g2p_plot.png", crispr_data_g2p_plot, device = "png", dpi = 450, width = 20, height = 4, units = "in")
Plot code:
ccle_drugs <- as.character(unique(ccle_data_g2p_genesfilt$Drug))
ccle_g2p_drugboxplots <- lapply(ccle_drugs, makeDrugBoxplots, dataset = "CCLE")
ccle_g2p_drugboxplots_paths <- paste0(ccle_drugs, "_ccle_drugboxplots.png")
pwalk(list(ccle_g2p_drugboxplots_paths, ccle_g2p_drugboxplots), ggsave, path = "./plots_18Q3/manuscript/ccle_g2p_drugboxplots", dpi = 450, width = 20, height = 4, units = "in")
Data management:
ccle_g2p_drugboxplots <- paste0(list.files("./plots_18Q3/manuscript/ccle_g2p_drugboxplots", full.names = TRUE))
names(ccle_g2p_drugboxplots) <- str_replace_all(ccle_g2p_drugboxplots, c("_ccle_drugboxplots.png" = "", "./plots_18Q3/manuscript/ccle_g2p_drugboxplots/" = ""))
bsselect(ccle_g2p_drugboxplots, type = "img", live_search = TRUE, show_tick = TRUE, height = 300, frame_height = 275)
Plot code:
ctrp_drugs <- as.character(unique(ctrp_data_g2p_genesfilt$Drug))
ctrp_g2p_drugboxplots <- lapply(ctrp_drugs, makeDrugBoxplots, dataset = "ctrp")
ctrp_g2p_drugboxplots_paths <- paste0(ctrp_drugs, "_ctrp_drugboxplots.png")
pwalk(list(ctrp_g2p_drugboxplots_paths, ctrp_g2p_drugboxplots), ggsave, path = "./plots_18Q3/manuscript/ctrp_g2p_drugboxplots", dpi = 450, width = 20, height = 4, units = "in")
Data management:
ctrp_g2p_drugboxplots <- paste0(list.files("./plots_18Q3/manuscript/ctrp_g2p_drugboxplots", full.names = TRUE))
names(ctrp_g2p_drugboxplots) <- str_replace_all(ctrp_g2p_drugboxplots, c("_ctrp_drugboxplots.png" = "", "./plots_18Q3/manuscript/ctrp_g2p_drugboxplots/" = ""))
bsselect(ctrp_g2p_drugboxplots, type = "img", live_search = TRUE, show_tick = TRUE, height = 300, frame_height = 275)
Plot code:
gdsc_drugs <- as.character(unique(gdsc_data_g2p_genesfilt$Drug))
gdsc_g2p_drugboxplots <- lapply(gdsc_drugs, makeDrugBoxplots, dataset = "gdsc")
gdsc_g2p_drugboxplots_paths <- paste0(gdsc_drugs, "_gdsc_drugboxplots.png")
pwalk(list(gdsc_g2p_drugboxplots_paths, gdsc_g2p_drugboxplots), ggsave, path = "./plots_18Q3/manuscript/gdsc_g2p_drugboxplots", dpi = 450, width = 20, height = 4, units = "in")
Data management:
gdsc_g2p_drugboxplots <- paste0(list.files("./plots_18Q3/manuscript/gdsc_g2p_drugboxplots", full.names = TRUE))
names(gdsc_g2p_drugboxplots) <- str_replace_all(gdsc_g2p_drugboxplots, c("_gdsc_drugboxplots.png" = "", "./plots_18Q3/manuscript/gdsc_g2p_drugboxplots/" = ""))
bsselect(gdsc_g2p_drugboxplots, type = "img", live_search = TRUE, show_tick = TRUE, height = 300, frame_height = 275)
ccle_g2p_order <- as.character(ccle_signif_g2p$Drug_Gene)
ccle_data_g2p$Drug_Gene_Ordered <- factor(ccle_data_g2p$Drug_Gene, levels = ccle_g2p_order, labels = sapply(strsplit(x = ccle_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
ccle_signif_g2p$Drug_Gene_Ordered <- factor(ccle_signif_g2p$Drug_Gene, levels = ccle_g2p_order, labels = sapply(strsplit(x = ccle_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
ccle_data_g2p_color <- as.character(ccle_data_g2p$Color_Nonsilent)
names(ccle_data_g2p_color) <- ccle_data_g2p$Mutation_Status_Nonsilent
ccle_label_text <- data.frame(p.signif.adj = ccle_signif_g2p$p.signif.adj, p.signif = ccle_signif_g2p$p.signif, Drug_Gene_Ordered = ccle_signif_g2p$Drug_Gene_Ordered)
ccle_data_g2p_plot <- ggplot(data = ccle_data_g2p, aes(x = Mutation_Status_Nonsilent, y = AUC)) +
facet_wrap(~ Drug_Gene_Ordered, drop = FALSE, nrow = 1) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(mapping = aes(fill = Mutation_Status_Nonsilent), position = position_dodge(0.85), outlier.shape = 3, outlier.size = 0.5) +
scale_fill_manual(values = ccle_data_g2p_color) +
guides(color = FALSE) +
geom_text(data = ccle_label_text, mapping = aes(x = 1.5, y = 7, label = p.signif), nudge_y = 0.1) +
theme(legend.position = "top", axis.ticks.x = element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank()) +
labs(title = "CCLE", fill = "Mutation Status", y = "AUC", x = "Mutation Status")
ccle_data_g2p_plot
# ggsave("./plots_18Q3/manuscript/ccle_data_g2p_plot.png", ccle_data_g2p_plot, device = "png", dpi = 450, width = 12, height = 4, units = "in")
ctrp_g2p_order <- as.character(ctrp_signif_g2p$Drug_Gene)
ctrp_data_g2p$Drug_Gene_Ordered <- factor(ctrp_data_g2p$Drug_Gene, levels = ctrp_g2p_order, labels = sapply(strsplit(x = ctrp_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
ctrp_signif_g2p$Drug_Gene_Ordered <- factor(ctrp_signif_g2p$Drug_Gene, levels = ctrp_g2p_order, labels = sapply(strsplit(x = ctrp_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
ctrp_data_g2p_color <- as.character(ctrp_data_g2p$Color_Nonsilent)
names(ctrp_data_g2p_color) <- ctrp_data_g2p$Mutation_Status_Nonsilent
ctrp_label_text <- data.frame(p.signif.adj = ctrp_signif_g2p$p.signif.adj, p.signif = ctrp_signif_g2p$p.signif, Drug_Gene_Ordered = ctrp_signif_g2p$Drug_Gene_Ordered)
ctrp_data_g2p_plot <- ggplot(data = ctrp_data_g2p, aes(x = Mutation_Status_Nonsilent, y = AUC)) +
facet_wrap(~ Drug_Gene_Ordered, drop = FALSE, nrow = 3) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(mapping = aes(fill = Mutation_Status_Nonsilent), position = position_dodge(0.85), outlier.shape = 3, outlier.size = 0.5) +
scale_fill_manual(values = ctrp_data_g2p_color) +
guides(color = FALSE) +
geom_text(data = ctrp_label_text, mapping = aes(x = 1.5, y = 22.5, label = p.signif), nudge_y = 0.1) +
theme(legend.position = "top", axis.ticks.x = element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank()) +
labs(title = "CTRP", fill = "Mutation Status", y = "AUC", x = "Mutation Status")
ctrp_data_g2p_plot
# ggsave("./plots_18Q3/manuscript/ctrp_data_g2p_plot.png", ctrp_data_g2p_plot, device = "png", dpi = 450, width = 12, height = 7, units = "in")
gdsc_g2p_order <- as.character(gdsc_signif_g2p$Drug_Gene)
gdsc_data_g2p$Drug_Gene_Ordered <- factor(gdsc_data_g2p$Drug_Gene, levels = gdsc_g2p_order, labels = sapply(strsplit(x = gdsc_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
gdsc_signif_g2p$Drug_Gene_Ordered <- factor(gdsc_signif_g2p$Drug_Gene, levels = gdsc_g2p_order, labels = sapply(strsplit(x = gdsc_g2p_order, split = "_"), function(x) paste0(x[1], "\n", x[2])))
gdsc_data_g2p_color <- as.character(gdsc_data_g2p$Color_Nonsilent)
names(gdsc_data_g2p_color) <- gdsc_data_g2p$Mutation_Status_Nonsilent
gdsc_label_text <- data.frame(p.signif.adj = gdsc_signif_g2p$p.signif.adj, p.signif = gdsc_signif_g2p$p.signif, Drug_Gene_Ordered = gdsc_signif_g2p$Drug_Gene_Ordered)
gdsc_data_g2p_plot <- ggplot(data = gdsc_data_g2p, aes(x = Mutation_Status_Nonsilent, y = AUC)) +
facet_wrap(~ Drug_Gene_Ordered, drop = FALSE, nrow = 3) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(mapping = aes(fill = Mutation_Status_Nonsilent), position = position_dodge(0.85), outlier.shape = 3, outlier.size = 0.5) +
scale_fill_manual(values = gdsc_data_g2p_color) +
guides(color = FALSE) +
geom_text(data = gdsc_label_text, mapping = aes(x = 1.5, y = 1, label = p.signif), nudge_y = 0.1) +
theme(legend.position = "top", axis.ticks.x = element_blank(), axis.text.x = element_blank(), axis.title.x = element_blank()) +
labs(title = "GDSC", fill = "Mutation Status", y = "AUC", x = "Mutation Status")
gdsc_data_g2p_plot
# ggsave("./plots_18Q3/manuscript/gdsc_data_g2p_plot.png", gdsc_data_g2p_plot, device = "png", dpi = 450, width = 12, height = 7, units = "in")
Match specific point mutations.
g2p_indications <- filter(read.delim("./data_munging/data_mutation_associations_appended.csv", sep = "\t", header = TRUE), Evidence.Level == "A")
maf_g2p_indications <- filter(maf_raw, Genome_Change %in% g2p_indications$MutationName)
crispr_g2p_indications <- merge(crispr_data_ptmuts, maf_g2p_indications, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
crispr_g2p_indications$Mutation_Status_Nonsilent <- ifelse(is.na(crispr_g2p_indications$Mutation_Status_Nonsilent), "Other", crispr_g2p_indications$Mutation_Status_Nonsilent)
dup_g2p_indications <- filter(crispr_g2p_indications[, c("Hugo_Symbol", "CCLE_Name", "Broad_ID")] %>% group_by(Hugo_Symbol, CCLE_Name, Broad_ID) %>% tally(), n > 1)
crispr_g2p_indications <- merge(crispr_g2p_indications, dup_g2p_indications, by = c("Hugo_Symbol", "CCLE_Name", "Broad_ID"), all.x = TRUE)
crispr_g2p_indications$Genome_Change <- factor(crispr_g2p_indications$Genome_Change, levels = unique(crispr_g2p_indications$Genome_Change))
crispr_g2p_indications_nonNA <- filter(crispr_g2p_indications, is.na(n))
crispr_g2p_indications_plot <- ggplot(crispr_g2p_indications, aes(x = Hugo_Symbol, y = Score)) +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(alpha = 0.5, color = "lightgray", outlier.shape = NA) +
geom_jitter(width = 0.3, mapping = aes(color = Mutation_Status_Nonsilent), size = 1) +
theme_light() +
theme(legend.title = element_blank()) +
labs(x = "Gene", y = "CERES Score")
crispr_g2p_indications_plot
crispr_g2p_indications_muts_plot <- ggplot(crispr_g2p_indications, aes(x = Protein_Change, y = Score)) +
facet_grid(~ Hugo_Symbol, scales = "free_x", space = "free") +
geom_hline(yintercept = 0, lty = 2, color = "darkgray") +
geom_boxplot(alpha = 0.5, color = "lightgray", outlier.shape = NA) +
geom_jitter(width = 0.1, mapping = aes(color = Mutation_Status_Nonsilent), size = 1) +
theme_light() +
theme(legend.title = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1)) +
labs(x = "Gene", y = "CERES Score")
crispr_g2p_indications_muts_plot
# ggsave("./plots_18Q3/manuscript/crispr_g2p_indications_plot_test.png", crispr_g2p_indications_plot, width = 12, height = 5, units = "in")
# ggsave("./plots_18Q3/manuscript/crispr_g2p_indications_muts_plot_test.png", crispr_g2p_indications_muts_plot, width = 20, height = 5, units = "in")
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., … Garraway, L. A. (2012). The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, 483(7391), 603–607. https://doi.org/10.1038/nature11003
Broad Institute Cancer Dependency Map; Cancer Data Science (2018): Cancer Dependency Map, CRISPR Avana dataset 18Q3 (Avana_public_18Q3). figshare. Fileset. doi:10.6084/m9.figshare.6931364.v1
Consortium, T. C. C. L. E., & Consortium, T. G. of D. S. in C. (2015). Pharmacogenomic agreement between two cancer cell line data sets. Nature, 528(7580), 84–87. https://doi.org/10.1038/nature15736
Data Science, Cancer (2018): DEMETER2 data. figshare. Fileset. doi:10.6084/m9.figshare.6025238.v2
Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., … Root, D. E. (2016). Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology, 34(2), 184–191. https://doi.org/10.1038/nbt.3437
Meyers, R. M., Bryan, J. G., McFarland, J. M., Weir, B. A., Sizemore, A. E., Xu, H., … Tsherniak, A. (2017). Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics, 49(12), 1779–1784. https://doi.org/10.1038/ng.3984
McFarland, J. M., Ho, Z. V., Kugener, G., Dempster, J. M., Montgomery, P. G., Bryan, J. G., … Tsherniak, A. (2018). Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. https://doi.org/10.1101/305656
print(sessionInfo())
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS 10.14
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] bindrcpp_0.2.2 forcats_0.3.0 stringr_1.3.1
## [4] dplyr_0.7.6 purrr_0.2.5 readr_1.1.1
## [7] tidyr_0.8.1 tibble_1.4.2 tidyverse_1.2.1
## [10] kableExtra_0.9.0 ggsignif_0.4.0 ggpubr_0.1.7.999
## [13] magrittr_1.5 ggplot2_3.0.0 data.table_1.11.4
## [16] bsselectR_0.1.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_0.2.4 haven_1.1.2 lattice_0.20-35
## [4] colorspace_1.3-2 htmltools_0.3.6 viridisLite_0.3.0
## [7] yaml_2.1.19 rlang_0.2.1 pillar_1.3.0
## [10] glue_1.3.0 withr_2.1.2 modelr_0.1.2
## [13] readxl_1.1.0 bindr_0.1.1 plyr_1.8.4
## [16] cellranger_1.1.0 munsell_0.5.0 gtable_0.2.0
## [19] rvest_0.3.2 htmlwidgets_1.2 evaluate_0.11
## [22] labeling_0.3 knitr_1.20 parallel_3.5.0
## [25] highr_0.7 broom_0.5.0 Rcpp_0.12.18
## [28] scales_1.0.0 backports_1.1.2 jsonlite_1.5.9000
## [31] hms_0.4.2 digest_0.6.15 stringi_1.2.4
## [34] grid_3.5.0 rprojroot_1.3-2 cli_1.0.0
## [37] tools_3.5.0 lazyeval_0.2.1 crayon_1.3.4
## [40] pkgconfig_2.0.1 xml2_1.2.0 lubridate_1.7.4
## [43] assertthat_0.2.0 rmarkdown_1.10 httr_1.3.1
## [46] rstudioapi_0.7 R6_2.2.2 nlme_3.1-137
## [49] compiler_3.5.0